Prime Institute of Public Health currently has three divisions that work under the direction of Director PIPH.

Postgraduate Programs, Policy and Research: This division caters for planning and development of curricula for various educational programs as well as course administration and programs management. The division also keeps liaison with the stakeholders for policy analyses and research.

Public Health Interventions and Research: This division is responsible for conception, planning, implementation and monitoring of all public health interventions.

Climate Change, Disaster Management & Research Unit: This division is mandated with conceptualizing, planning, implementing and evaluating the Climate Change & Disaster Management related grants and projects.