NFRDI recognizes that partnerships and collaborations are essential to its success as a leading fishery research institute. To align and harmonize fishery research and development efforts in the country, NFRDI actively works with the following partners:

• Department of Agriculture-Bureau of Agricultural Research (DA-BAR),
• Department of Science and Technology-Philippine Council for Agriculture, Aquatic and Natural Resources Research and Development (DOST-PCAARRD),
• Southeast Asian Fisheries Development Center/Aquaculture Department (SEAFDEC/AQD),
• academe,
• local government units, and
• other stakeholders.

NFRDI also works with international organizations such as the:

• United States Agency International Development (USAID) Fish Right,
• Smithsonian Institution Natural Museum of Natural History,
• Western and Central Pacific Fisheries Commission, and
• United Nations Environment Programme, among others.