In order to satisfy the broad needs for advancing cutting-edge research, NIFS conducts six collaboration research programs. These are : General Collaboration Research which utilizes the facilities of NIFS, Fundamental Facility Type Collaboration Research, Fusion Development Collaboration Research, Subject Proposal Type Collaboration Research, Core Proposal Type Collaboration Research, and Fusion DEMO Reactor Collaboration Research which utilize the facilities of other institutes. The joint use and joint research activities are powerfully developed by accepting research proposals from researchers each year.

General Collaboration Research is a system for the collaborators to carry out their research by using the facilities or the resources of NIFS, including experimental devices, diagnostics, the supercomputer, databases, and others. Because nuclear fusion includes a wide research area in physics and technology, from fundamental research to application, the system has a variety of categories.

In this collaboration, the collaborators come to NIFS and carry out research at NIFS. However, if it is necessary, NIFS staff can go to the university of a collaborator to perform joint research there. Furthermore, in the "network-type collaboration" category, the collaborators may conduct experiments at other universities involved in a particular project.

Many exploratory research proposals are adopted in the General Collaboration Research, and since a graduate student can be a collaborator, it is useful for training young researchers.

In Fundamental Facility Type Collaboration Research, excellent and original joint research that will contribute to the development of fusion science is conducted between NIFS and five research centers, the Plasma Research Center at the University of Tsukuba, the Laboratory for Complex Energy Processes at Kyoto University, the Institute of Laser Engineering at Osaka University, the Advanced Fusion Research Center at Kyushu University, and the Hydrogen Isotope Research Center, the Organization for Promotion of Research, at the University of Toyama

Fusion Development Collaboration Research aims to strengthen international competitiveness in the field of fusion science and to strengthen the foundation for human resource development. Fusion Development Collaboration Research promotes academic research using state-of-the-art fusion plasma experiment devices such as JT-60SA led by National Institutes for Quantum Science and Technology (QST) through the joint use program. Fusion Development Collaboration Research strengthens collaboration between academic research and fusion development research through the cooperation of NIFS units and researchers in the field of fusion science and a wide range of academic circles.

In Subject Proposal Type Collaboration Research, joint research using the facilities and equipment of domestic and overseas universities and related research institutions as a research platform, and network-type joint research in which multiple universities collaborate ,is conducted.

In Research Core Proposal Type Collaboration Research, multiple universities and related research institutes collaborate on important issues in the field of fusion science to conduct joint research aimed at creating universal academic and technical knowledge and strengthening the research capabilities of the community through the creation of strong research teams.

This collaboration program was initiated in fiscal year 2019 as the fourth category of the collaboration programs conducted by NIFS to accelerate the "action plan towards fusion DEMO research and development", which was composed by the Taskforce on DEMO Comprehensive Strategy in the Ministry of Education, Culture, Sports, Science and Technology (MEXT). This program attempts to solve issues of the “action plan", together with the collaboration programs conducted by the National Institutes for Quantum Science and Technology (QST).