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In 1900, the Russians formed a temporary flotilla on the Amur river out of private steamers and barges. Initially, it served transportation purposes during the Russo-Japanese War of 1904-5. Officially, the AMF was created in July 1906 for the purpose of defending the border line of the Amur basin and securing water communication on the Amur river. In 1910, the AMF comprised 28 units, including eight turret gunboats and ten smaller gunboats. In December 1917, they formed the Soviet Amur military flotilla, which would take part in the Russian Civil War.
In 1918, the AMF was captured by the Japanese, who took away almost all of the ships in May 1920. With the end of the Civil War in the Far East, the Soviets began reconstruction of the flotilla. In 1925-6, it grew bigger with the return of the ships, taken away by the Japanese. In 1929, the AMF included four river monitors and other ships. In 1930, the AMF was awarded with the Order of the Red Banner for its successful military operations during the Sino-Soviet conflict of 1929.
Neon Vasilyevich Antonov (1907-1948) was transferred to command the flotilla, in preparation for the war against Japan. During the operation, the AMF (eight monitors, eleven gunboats, 52 armored launches etc.) under the command of N. V. Antonov cooperated with the armies of the 1st and the 2nd Far Eastern fronts on the rivers of Amur, Ussuri, Sungari, and Lake Khanka.
Amur Military Flotilla was disbanded on 7 June 1998.