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This paper aims to identify the strengths of the universities based on the research area which are prioritized by the Government of Indonesia in the National Medium Term Development Plan 2015–2019, in the research areas of food and agriculture; energy, new and renewable energy; health and medicine; transportation; telecommunication, information and communication; defense and security technologies and advanced materials.

The mapping of the research strength in Indonesian universities is performed by using data of the university research output in the Information System for Research and Community Service, Ministry of Research, Technology and Higher Education and categorized into seven categories, i.e. accredited national journals, international journals indexed by Scopus or others, Intellectual Property ownership, textbooks, prototypes and an appropriate technology. Based on the data obtained from Information System for Research and Community Service, there are 904 universities in Indonesia conducting research activities and generating 14,188 research outputs.

This paper analyzes 3 of the 9 National Research Priorities, namely, food, energy and health and medicine. The data show that there are 904 universities in Indonesia conducting research activities and producing 14,188 research results. The research strength index based on National Research Priorities shows that three universities have the highest cluster strength index. Gadjah Mada with an index value of 4.95 is the highest index in the food cluster. In the energy cluster of the Institut Teknologi Bandung with the highest index value of 0.63. Meanwhile, the Universitas Indonesia reached 2.06 as the highest index value in the health and medicine cluster.

Measurement of the strength of the study was conducted using data from research results from universities in 2016 which were recorded in the Information System for Research and Community Service. The University’s R&D strength is calculated from seven categories of research results: accredited national journals, international journals indexed by Scopus or others, intellectual property rights, textbooks, prototypes and appropriate technology products.

The purpose of this study is to outline the improvement of framing in Indonesia science and technology policy content, policy formulation model, policy strategy implementation and policy performance indicators.

This study is conducted by implementing action research model to generate new knowledge as a research interest, through the search for solutions or improvements to problematical situation, applying Soft Systems Methodology. Thus, this research model is regarded as Soft Systems Methodology-based Action Research (SSM-based AR).

Policy formulation is not evidence based in which policy documents remain theoretical and are impractical or not detailed in engaging real conditions and strategic issues, yet the targets are measurable despite predictive results. Change and strengthening are required in the national science and technology policy for the next period, on the basis that future research policies are encouraged to address problems and solutions to build a country based on science and technology. Indonesia requires policies involving both effective and efficient national research; therefore, the need for an integrated policy direction conveying science and technology and other related sectors, such as the health sector and food, remains vital.

Previously, science and technology policy planning in Indonesia was not equipped with data and indicators of success, having no target to achieve within a five-year period. In the coming periods, science and technology policy documents in Indonesia are issued in the form of government regulations/presidential decrees, including indicators of science and technology achievements (quantitatively) for five years.

This paper aims to identify and classify the parameters that construct the input, processes, output, productivity and outcome variables that affect performance. These parameters are used in the evaluation model to measure research performance in universities so that they can be used as the basis for making leadership policies both at the national and institutional levels.

The design of this research is a quantitative research method using a survey questionnaire that was sent to the heads of research institutions at universities in Indonesia. To obtain these parameters, a test for determining the value of the loading factor was used.

The authors found that input variable parameters consisted of 10 parameters; process variable consisted of 22 parameters; output variable parameters consisted of 8 parameters; productivity variable consisted of 4 parameters; and outcome variable parameters consisted of 10 parameters.

One approach to obtain parameters is through systems theory, where every element that makes up the organization contributes to the achievement of goals. This study attempted to develop parameters in the performance appraisal model of systems theory-based research institutions that are adapted to trends in the direction of research in universities. These parameters are based on aspects of input, process, output, productivity and outcome.