Militarization was another aspect of the Soviet state. Large parts of the country, especially the coastal areas, were closed to all but the Soviet military. Most of the sea shore and all sea islands (including Saaremaa and Hiiumaa) were declared "border zones". People not actually residing there were restricted from travelling to them without a permit. A notable closed military installation was the city of Paldiski, which was entirely closed to all public access. The city had a support base for the Soviet Baltic Fleet's submarines and several large military bases, including a nuclear submarine training centre complete with a full-scale model of a nuclear submarine with working nuclear reactors. The Paldiski reactors building passed into Estonian control in 1994 after the last Russian troops left the country. Immigration was another effect of Soviet occupation. Hundreds of thousands of migrants were relocated to Estonia from other parts of the Soviet Union to assist industrialisation and militarisation, contributing an increase of about half a million people within 45 years.

What political strategy only allowed major parts of of Estonia to be accessed by the Soviets?