NOAA's Office of National Marine Sanctuaries has primary responsibility for the management of Papahānaumokuākea National Marine Sanctuary pursuant to the National Marine Sanctuaries Act. As the sanctuary includes state waters, NOAA co-manages Papahānaumokuākea National Marine Sanctuary with the state of Hawaiʻi. NOAA also manages the sanctuary in partnership with the U.S. Fish and Wildlife Service and the Office of Hawaiian Affairs.

The Native Hawaiian community is a critical part of the co-management structure of Papahānaumokuākea Marine National Monument through the Office of Hawaiian Affairs. The memorandum of agreement that incorporates the Office of Hawaiian Affairs as a monument co-trustee will continue to serve as the guiding document on the integration of the national marine sanctuary into the monument co-management structure.
The co-management structure of Papahānaumokuākea Marine National Monument has not changed as a result of the designation of a national marine sanctuary. NOAA's Office of National Marine Sanctuaries has been a key partner and co-managing agency in the management of Papahānaumokuākea since the initial designation of the Northwestern Hawaiian Islands Coral Reef Ecosystem Reserve in 2000. NOAA's Office of National Marine Sanctuaries will continue to work collaboratively with the Papahānaumokuākea Monument Management Board to:
- Conduct, support, and promote research
- Characterize and monitor (long term) marine ecosystems and species
- Characterize and monitor (long term) cultural and maritime heritage resources