The National Command Structure was activated with the President as the National Commanding Authority and the IATF acting as the primary policy-making body. This is chaired by the Secretary of Health with the Cabinet Secretary and the Secretary of Environment and Natural Resources as co-chairs.

Strategic operations were organized under the National Task Force chaired by the Secretary of National Defense, co-chaired by the Secretary of Interior and Local Government.

Operations response was delegated to the National Incident Commander (NIC). The NIC is chaired by the Office of the Presidential Adviser on the Peace Process, with the Bases Conversion and Development Authority President and CEO as Deputy.

The tactical response has since been re-organized into three main clusters: 1) Response Cluster headed by the DOH; 2) Vaccine Cluster headed by the Vaccine Czar and concurrent National Chief Implementer from the OPAPP, and 3) The Recovery Cluster headed by NEDA. Representatives from the different agencies comprise these clusters and are coordinated with regional, provincial, city, and municipal counterparts, reporting to the NIC.

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