The National Research Institute began when The Australian National University opened its New Guinea Research Unit (NGRU) in Badili, a surburb of the National Capital District in 1961.

Then in 1968, the NGRU moved to its new site in Waigani, opposite the University of Papua New Guinea. The NGRU's research focused on internal migration and urbanisation, and land use and productivity. It also covered social science research in the fields of politics, anthropology, geography, and linguistics. However, the Unit was more focused on issues of policy relevance to Papua New Guinea.

Over the years, the NGRU produced an impressive body of research findings. As Papua New Guinea moved towards achieving Independence, The Australian National University decided to hand the Unit over to the Papua New Guinean Government. Soon after gaining Independence in 1975, the NGRU became an independent statutory authority, reporting to the National Parliament as the Papua New Guinea Institute of Applied Social and Economic Research (IASER).

The IASER continued the NGRU's practical, policy-oriented research programs, and expanded the scope of its reports to include monographs, discussion papers, special reports, bibliographies, and indexes. In line with the national government's higher education plans, the IASER (Amendment) Bill was introduced in 1998 and this saw the merging of the activities of the Institute of PNG Studies and the Education Research Institute (University of Papua New Guinea), with those of the IASER. As a result, the range of reports and publications was again expanded to include areas such as education, literature, social history, and music.

In 1989, Cabinet approved a name change, from IASER to the National Research Institute (NRI). The National Research Institute was confirmed by the Papua New Guinea IASER (Amendment) Act in May 1993, and is now an independent statutory authority.