Following the Japanese occupation of the Dutch East Indies, the Department of Economic Affairs was dissolved, and Subekti became unemployed. His unemployment ended in 1943 when he entered the Naval Institute in Semarang and was put in command of one of its training ship. After the independence of Indonesia, all Japanese-established institute in the country was dissolved, including Subekti's Naval Institute. Subekti then joined the newly formed Indonesian Navy and became a coordinating officer on 23 August 1945.