Study design and context

To assess the current status of Indonesia’s NHRS, a qualitative approach was used to explore stakeholders’ perspectives. In this study, “health research” was defined as any research activities that contribute to the strengthening of the health system, improving population health, and informing evidence-based health policy [14]. This includes biomedical, clinical, public health, and health systems research conducted by government institutions, universities, and research organisations at both national and subnational levels. The scope also encompasses research related to health policy, governance, financing, and innovation that supports the broader objectives of national health development.

Since 2020, Indonesia’s research ecosystem has been primarily managed by two key institutions: BRIN and the Ministry of Higher Education, Science and Technology (Kementerian Pendidikan Tinggi, Sains, dan Teknologi, Kemendikti-Saintek). BRIN is a centralised agency established through the merger of several previous research institutions. Previously, health-related research had been managed by the Health Research and Development Agency (Badan Penelitian dan Pengembangan Kesehatan, Balitbangkes) under the Ministry of Health (Kementerian Kesehatan, Kemkes), the Eijkman Institute, the Indonesian Institute of Sciences (Lembaga Ilmu Pengetahuan Indonesia, LIPI), and other agencies, while Kemendikti-Saintek oversees the research conducted by universities and colleges. Both BRIN and Kemendikti-Saintek operate directly under the president [16]. In addition to these two institutions, the Ministry of Religious Affairs (Kementerian Agama, Kemenag) coordinates religion-based universities and colleges, which also conduct research activities. On the funding side, domestic research funding increasingly comes from the Indonesia Endowment Fund for Education Agency (Lembaga Pengelola Dana Pendidikan, LPDP), which plays an expanding role in supporting national research and innovation.

Participants’ selection and recruitment

Participants were selected using purposive sampling to ensure representation from key stakeholders involved in the governance and implementation of health research in Indonesia. Eligible participants were individuals with demonstrated experience in research management and policy at national, subnational, and institutional levels (Table 1). This included academic stakeholders holding at least a lecturer-level position (or equivalent), as well as policymakers occupying leadership roles (heads of units, divisions, or departments). To ensure a strategic and informed perspective, the study prioritised senior representatives with a minimum of five years of relevant experience in their respective fields.

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Table 1. List of participants.

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To ensure geographic diversity, invitations were extended to central government agencies and academic institutions from Western, Central, and Eastern Indonesia. At the national level, four key policymaking institutions were represented: the Health Research Organisation of the BRIN, the Deputy for Regional Research and Innovation (Badan Riset dan Inovasi Daerah, BRIDA) under BRIN, the Health Development Policy Agency of the Ministry of Health (BKPK-Kemenkes), and the Kemendikti-Saintek.

From the institutional level, participants were drawn from universities and research institutes engaged in research planning and management. The academic cohort included two participants from Western Indonesia, two from Central Indonesia, and four from Eastern Indonesia. Most were affiliated with medical faculties or research centres, providing perspectives on institutional-level research management and subnational health research needs. These academicians were specifically selected for their leadership roles in organising and executing health research, particularly in relation to national research funding and programme alignment. Efforts were made to ensure diversity in institutional roles, gender, and subnational representation in line with purposive sampling goals.

The participant recruitment period was conducted from 20/05/2024–30/05/2024. The sample size was predetermined during the study design. All eligible key informants received formal invitations via e-mail, accompanied by an explanation of the study objectives. Follow-up communication by phone or text was conducted within two to three days to confirm participation.

Data collection

Data were collected through an expert panel meeting and key informant interviews. The expert panel meeting was conducted on 31/05/2024 in a hybrid format, held in person at the Faculty of Medicine, Universitas Indonesia, and online via Zoom to enable broad participation and reduce logistical constraints. The hybrid approach is feasible and valid in qualitative policy research involving geographically dispersed participants [17].

Of the 13 stakeholders invited, 11 attended the expert panel meeting. Those who were unable to participate were subsequently invited for individual key informant interviews, which were conducted on 13/12/2024 and 16/12/2024. Additional interviews were also conducted with selected participants who were considered to have in-depth insights essential for achieving a comprehensive understanding of Indonesia’s NHRS. All participants provided written informed consent, and sessions were audio-recorded with permission. Data saturation was reached when no new themes or insights emerged during the final interviews.

The expert panel was facilitated by the principal investigator (TD) to discuss four main areas: (a) how institutions set health research priorities, (b) stakeholders involved in the process, (c) challenges in conducting and implementing research aligned with national priorities, and (d) critical enablers and barriers in strengthening Indonesia’s health research system. We conducted and transcribed verbatim the discussion and interviews in Bahasa Indonesia. The transcripts were securely stored and only accessible to the researchers.

Data analysis

Transcripts were later imported into NVivo (version 12). Analysis was conducted using the Framework Method [18] and guided by the NHRS framework [19], consisting of four core domains: governance, financing, creating and sustaining resources, and producing and using research (Table 2). This framework served as the analytical foundation to understand the functions, dynamics, and coordination of Indonesia’s health research system. A combination of deductive and inductive analysis was applied. The Steps for Coding and Theorization (SCAT) method [20] was employed, as it is well-suited for small-to-medium qualitative datasets. Initial coding was independently conducted by two researchers (FQ and DA). Any discrepancies were resolved through discussions until consensus was achieved. Codes were then synthesised into subthemes and grouped into broader themes aligned with the NHRS framework.

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Table 2. Domains of NHRS.

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Data were triangulated across multiple sources. Documentary data were used to map the structural and institutional landscape of the NHRS, while interview data from expert panel discussions and key informant interviews provided contextual insights into how these structures function in practice. The integration of these data sources enabled both validation of documented evidence and the identification of gaps between formal arrangements and operational realities.

In addition, the analysis incorporated selected domains from the Questionnaire on Country Resources for Health Research [21], a tool developed by the WHO (S1 Appendix) and previously assessed in the WHO Africa Region [14,15]. Of the ten categories in the original questionnaire, we only assessed Indonesia’s NHRS using seven categories that are relevant and applicable to the Indonesian context: health research policy, legislation, strategic planning, coordination mechanisms, research programmes, research institutes, and financing and budgeting. Two researchers (FQ and DA) completed the questionnaire items based on publicly available data sources.

Representative quotes were identified and translated from Bahasa Indonesia into English, followed by back-translation to preserve meaning and contextual nuance. Finally, several team meetings were held as part of the triangulation process to refine themes according to the NHRS framework and validate interpretations. Inconsistencies in categorisation were discussed and reconciled.

Ethics

Ethical clearance was obtained from the Health Research Ethics Committee, Faculty of Medicine, Universitas Indonesia, No. KET-658/UN2.F1/ETIK/PPM.00.02/2024. Written informed consent was obtained from all participants in the study.

Current state of NHRS in Indonesia

At the national level, BRIN serves as the central body coordinating research and innovation across all sectors, including health. BRIN oversees subnational research bodies, known as BRIDA, which function to link national research priorities with subnational implementation (Fig 1). Guided by its Strategic Plan 2022–2024 (BRIN Regulation No. 6 of 2023), one participant (N03) noted that “BRIN performs a distinctive triple role: as a funder, implementer, and policy advisor—a governance model which is rarely observed internationally.”.

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Fig 1. Current governance landscape of Indonesia’s health research ecosystem.

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The Ministry of Health primarily focuses on translating research into health policy and practice through its policy and ethics bodies, including BKPK-Kemkes and the National Ethical Committee for Health Research, as well as through clinical and public health research infrastructures such as the Indonesia Clinical Research Center (INA-CRC) and public health laboratories.

The Ministry of National Development Planning (Kementerian Perencanaan Pembangunan Nasional, Bappenas) aligns health research activities with the country’s medium and long-term development goals. Research within higher education institutions is governed by Kemendikti–Saintek, through the Directorate of Research and Development and the Higher Education Service Institutions, overseeing both public and private universities and their affiliated research centres. In parallel, Kemenag manages religious higher education institutions, such as Islamic universities, which also conduct research and contribute to the national health research ecosystem.

In terms of financing, health research in Indonesia is supported through two main funding streams. First, BRIN manages national competitive research funding through several schemes. These schemes are primarily funded by the Indonesia Endowment Fund for Education (Lembaga Pengelola Dana Pendidikan, LPDP), offer relatively larger budgets, and are open year-round, although they generally require the involvement of BRIN researchers. Second, BRIN also provides funding through internal schemes managed by individual Research Organizations and largely financed through the state budget (Anggaran Pendapatan dan Belanja Negara, APBN).

In the health sector, these function as seed funding with stricter eligibility criteria, requiring BRIN researchers to serve as principal investigators. In parallel, universities access research funding through Kemendikti–Saintek via institutional research offices (Lembaga Penelitian dan Pengabdian kepada Masyarakat, LPPM); however, these funds are comparatively limited. Overall, while BRIN, particularly through LPDP-funded schemes, constitutes the main source of national research funding, APBN-based allocations remain constrained and subject to annual budget negotiations.

At the subnational and local levels, most operational research is conducted by BRIDA, universities, and health research centres. In addition, independent research institutions and private-sector actors, including industry-based research units and contract research organisations, also contribute to research activities, particularly in applied and clinical research. The overview of Indonesia’s NHRS is presented in Table 3.

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Table 3. Current situation and challenges of Indonesia’s NHRS.

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Governance

The governance of health research in Indonesia is shaped by a combination of policies, legal frameworks, and institutional arrangements intended to align research activities with national health priorities. While Indonesia has an established national health policy articulated in the national development plans and is planned to be operationalised through the Health Sector Master Plan (Rencana Induk Bidang Kesehatan, RIBK), an explicit and integrated national health research policy has not yet been formalised. As mentioned by a participant (N04): “To identify which health topics or sectors could potentially be collaborated on with universities, we encourage academics to refer to existing strategic documents, such as the RPJMN and the Health Sector Master Plan (RIBK). We expect these documents to serve as a reference for academics to identify what roles and research topics can be pursued in collaboration with the government.”

As one informant (N02) explained, “The Ministry of Health is currently developing RIBK, which is derived from the health sector medium-term plan. This document identifies the indicators and activities required to achieve the targets and is expected to serve as a reference for academics in identifying potential roles and research topics.” While RIBK provides an important reference, its role is primarily indirect because it targets the health sector as a whole rather than a national health research plan.

Health research governance is further supported by several legal and regulatory frameworks, including the Health Law, Government Regulation No. 28 of 2024, and the Ministry of Health Regulation on Health Research and Development Ethics Committees. Collectively, these regulations established ethical standards and institutional responsibilities, along with the formal basis for research governance.

The absence of a dedicated and integrated research policy has resulted in limited complementarity between health and research agendas at the national level. This is reflected in the fragmented coordination across multiple research institutions which have their own research priorities. Another challenge in the governance domain is the limited coordination between national and subnational levels. The current Indonesian NHRS plan remains highly centralised, with agenda-setting dominated by top-down mechanisms derived from national medium- and long-term development plans (N04, N03) “There’s no single body to coordinate or monitor how all these research institutions work together (N03).”

Financing

Indonesia’s health research financing is primarily sourced from the state budget, distributed through BRIN and Kemendikti-Saintek. BRIN manages eight research funding schemes and submits proposals to Bappenas as part of the national planning cycle. Each institution, such as BRIN, Kemendikti-Saintek, and Kemkes, operates its own funding mechanisms. As one participant noted (N01), “Government research funding is actually spread across many institutions, such as higher education, BRIN, LPDP, and even industry. However, these allocations tend to operate separately, without integrated coordination. They all run on their own.”

Moreover, the total funding for health research remains low, forcing many researchers to seek external sources, such as international donors (e.g., e-Asia, International Atomic Energy Agency (IAEA), and WHO), which are highly competitive and limited in scope. Participants also mentioned having to use out-of-pocket funding for publication due to a limited budget. One participant (N03) described, “Basic research needs publication fees or conference attendance, which are often not covered. Researchers end up using their own funds or university funds, even though publications are used as performance indicators.”

Further compounding the issue, BRIN’s grant requirements often mandate collaboration with BRIN-affiliated researchers, reducing inclusivity and discouraging independent or locally driven research. Although dissemination efforts to promote funding schemes have increased, other participants emphasised persistent funding constraints and delayed access to grant information, particularly in peripheral regions. As one respondent (W01) noted, “Limited funding strongly affects our ability to conduct high-quality research. Important information often reaches us late, and sometimes we only learn about grant competitions after they have already closed.”

Creating and sustaining resources

Indonesia has made significant investments in research infrastructure, such as the availability of PET scan facilities and non-human primate laboratories under BRIN. While these facilities represent high-end research capacity, access remains limited, primarily to researchers within BRIN-affiliated institutions. Collaboration with BRIN is a prerequisite for grant eligibility and infrastructure access. External researchers need to collaborate with BRIN scientists to access their advanced facilities, which pose logistical and bureaucratic hurdles.

Furthermore, participants also expressed the mismatch between the availability of research infrastructure and expertise. BRIN has conducted outreach to universities regarding its research grant schemes, as well as non-financial support, including access to research equipment, talent management programmes and knowledge networks to address capacity gaps. One participant (N03) mentioned, “BRIN does conduct intensive outreach activities. As heads of research organisations, we also help disseminate information about available funding schemes, as well as non‑funding programmes such as talent management, scholarships, and related opportunities.” BRIN has also introduced seven thematic health research centres under its coordination.

Resource sharing across institutions is often constrained by unclear resource sharing mechanisms, limited interoperability between research management systems, and siloed data infrastructures. Many researchers, particularly those based outside Java Island, reported limited awareness of the existing outreach programmes. As one participant (W02) said, “Limited funding is one of the factors that affects our ability to conduct high‑quality and productive research in Aceh, especially since we are located at the westernmost edge of the country. This has been a recurring challenge for us, partly because we are located at the edge of Sumatra and our alumni network is still limited.” Importantly, BRIN informants acknowledged the information gaps, recognising that outreach mechanisms may not sufficiently reach all institutional levels.

Some participants also highlighted structural and infrastructural constraints that further limited their research capacity, noting that even when equipment was available, it was often unusable due to inadequate infrastructure and supporting facilities. One participant (E01) stated, “Basic research tools like PCR and electrophoresis are very challenging for us to use. Sometimes the equipment exists, but the electricity capacity is insufficient, or reagents are difficult to procure.”

Producing and utilising research

Current Indonesian health research institutions emphasise output-driven research through publications, patents, technology readiness levels (TRL), and prototype development, particularly within universities and national research institutions. These outputs are recognised as indicators of research productivity. Although universities produce a substantial volume of health research, their work is rarely integrated into national policy processes. A participant described how studies often remain disconnected from decision-making: “Many studies stay as reports. They are completed, but there is no clear pathway for them to enter the policy process.” (N01) Participants argue that this may also be influenced by the limited participation of policymakers and knowledge implementers in the production phase of research.

Indonesia has shown progress in strengthening formal institutions and national surveys to support research production and utilisation. Health Technology Assessment (HTA) is perceived as a promising platform for research translation for BRIN, universities, industries, and hospitals. The HTA Committee was established to improve the uptake of research products into the health system by formulating recommendations, especially for the national health insurance. The MoH also has several large-scale research initiatives to inform national health planning and policy formulation, including Basic Health Research (Riset Kesehatan Dasar, Riskesdas), the Health Research Survey (Survei Kesehatan Indonesia, SKI), and the Indonesian Nutritional Status Survey (Survei Status Gizi Indonesia, SSGI). The SKI integrates Riskesdas and SSGI to assess health development achievements over the past five years and monitor trends in child nutrition, producing data representative from national to district levels. Other formal institutions were also established to bridge clinical application and policy translation, such as the Indonesian Clinical Research Unit and Health Development Agency. However one informant mentioned about the challenge of translating research into policy, “Unfortunately, there are many limitations to the access for research outputs. There are many research outputs, but we don’t know how to access them for HTA and research translation.” (N05).

Strengths

This paper contributes to the limited literature on the NHRS in low and middle-income countries. By examining the Indonesian context, it may reflect similar NHRS challenges identified in other LMIC settings. This study proposes context-specific recommendations, including the need for a unified research roadmap, coordination mechanisms, and strengthened subnational research bodies to bridge national strategies with local needs. Further research across other countries is essential to inform NHRS development and encourage context-based reforms in similar settings.

Limitations

The findings of this study should be interpreted cautiously with the following limitations. First, variations in governance and decision-making structures among institutions involved in health research in our context may influence the interpretation and applicability of our findings. Second, data collection was conducted in a hybrid format, which may have affected the dynamics of interaction and limited equal participation opportunities between in-person and virtual attendees. Third, the findings are contextual in our setting, which limits the generalisability. Given these limitations and the complexity of policy and institutional contexts, further research to explore the NHRS in other LMICs is necessary to support policy recommendations.