On 3 November, 1918, the Ottoman Imperial Navy Fleet Commander ordered all flags to be struck on all warships lying in the Golden Horn, and the Ottoman Imperial Navy ceased to exist. The warships were disarmed during the last week of 1918.

• During this period, only a small number of former Ottoman Imperial Navy vessels were allowed by the Allies to remain on active coast guard duties and were released from internment on 26 February 1919.
• During the early stages of the Turkish War of Independence, these two gunboats did not return to Istanbul, despite heavy pressure from the Ottoman government and the Allies. Instead, they were placed under the command of the Turkish liberation forces and headquartered in Ankara.
• A large number of the naval officers and students of the Naval Academy went to Anatolia to participate in the War of Independence.

On 10 July 1920, the Directorate of Naval Affairs (Umur-u Bahriye Mudurlugu) was founded in Ankara under the Ministry of National Defense and was given the duty of organizing and maintaining strategic logistical shipping through the Black Sea in order to provide the Turkish Nationalist Army forces in Anatolia with weapons and other supplies. All existing naval institutions in the parts of Anatolia that were administered by the Ankara government were assigned to this Directorate.

On 1 March 1921, the Directorate of Naval Affairs was transformed into the Presidency of the Naval Department (Bahriye Dairesi Reisligi) and had control over the following Naval Commands:

• Samsun, Amasra and Izmit (formed on 28 June 1921);
• The Naval Transport Detachment in Trabzon;
• The Naval Transport Command in Eregli;
• The Naval Detachment in Lake Egirdir; and,
• The Naval Liaison Group in Fethiye (formed on 16 March 1921).
• Following the Armistice of Mudanya on 11 October 1922, the former Ottoman Ministry of the Imperial Navy (Bahriye Nazırlıgı) building in the Kasımpasa quarter of Istanbul, on the Golden Horn, became the headquarters of the Istanbul Naval Command on 14 November 1922.

Film taken in the www.britishpathe.com arcival films of the "Turkish Army makes triumphal entry into Constantinople" (dated 1920), shows Turkish civil officials wearing striped coloured armbands (a typically British Army practice); these are likely to be British appointed officials employed to maintain the Constantinople Government Authorities, during the Allied occupation of the city.

In the same period, a number of Turkish civilian seamen formed a group under the name of the Naval Aid Organization (Muavenet-i Bahriye), to secretly obtained cannons, light weapons, ammunition, landmines and ordnance from the former Ottoman military warehouses in Istanbul that were under the control of the occupying Allies and sent them in to Anatolia with civil water transportation crafts.