PRiSM operates in a multi-tiered scheme starting from the national to regional and institutional engagement. It serves as the center of operations, management, coordination, and collaboration. 

At national level, PRiSM Unit under the Agronomy, Soils, and Plant Physiology Division (ASPPD) of PhilRice receives policies, general directions, and other instructions from DA-Field Operations Service (FOS) and works in coordination with the Field Programs Operational Planning Division (FPOPD), Disaster Risk Reduction (DRRM), and Information and Communications Technology Service (ICTS).

At regional level, operations  is led by a focal person under the DA-RFOs and is coordinating with  PRiSM Unit at PhilRice for implementation protocols and directions.