RIMES is governed by the Council, composed of heads of National Meteorological and Hydrological Services (NMHSs) as well as national scientific and technical agencies generating multi-hazard early warning information. The council is empowered to make policy decisions on behalf of governments, concerning regional early warning arrangements. The Secretariat carries out the decisions and tasks assigned by the Council and provides support to the Program Unit in managing the regional early warning facility. Currently, the Government of India serves as the Council Chair, and Maldives as the Secretariat. The RIMES Ministers Conference, established in 2012, provides policy and resource mobilization support.

The Program Unit is responsible for the daily operation and management of the regional early warning facility, and the implementation of programs and activities. The Program Unit has financial and administrative autonomy through powers delegated by the RIMES Council. The Program Unit is co-located with RIMES regional early warning facility.