The Estonian Internal Security Service is headed by the Director General of the Estonian Internal Security Service. Since June 2013 the Director General of the Estonian Security Police is Arnold Sinisalu.

The Director General of the Internal Security Service has three deputies.

The structural units of the Estonian Internal Security Service are departments and divisions.

Estonian Internal Security Service has three regional departments:

  • Southern Department (service area: Valga County, Võru County, Viljandi County, Tartu County, Jõgeva County and Põlva County)
  • Virumaa Department (service area: Lääne-Viru County and Ida-Viru County)
  • Western Department (service area: Hiiu County, Saare County, Lääne County, Rapla County Järva County and Pärnu County)