Following the Japanese occupation of the Dutch East Indies, the Department of Economic Affairs was dissolved, and Subekti became unemployed.

[1] His unemployment ended in 1943 when he entered the Naval Institute in Semarang[2] and was put in command of one of its training ship.

[3] During his early tenure in the navy, Subekti helped form the Marine Corps, which at that time was a special unit under the command of Tegal Naval Base.

Subekti — at that time ranked sea major — was inaugurated as the Commander of the Marine Corps on 15 November 1945 with Naval Captain OB Sjaaf as his deputy.

Subekti returned to Indonesia and became the chief of staff of the Surabaya Maritime Region, an office he previously held in acting capacity.

[2] Subekti received his first and only political appointment when he briefly became the Vice Governor of West Irian.

[2] During his tenure in the development command, Subekti led an orientation visit to the United States Navy.

[2] As part of the dual function of the armed forces at that time, Subekti was ex officio appointed to civilian offices, such as member of the Functional Regional Council and a member of the People's Consultative Assembly from the Armed Forces.