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Commander Naval Activities Japan (COMNAVACT JAPAN) was established on January 19, 1946 in Yokohama to control Naval Shore Activities in Japan. In February 1946 U.S. Fifth Fleet came under control of COMNAVACT Japan.

Commander Naval Forces, Far East (COMNAVFE) was established on January 1, 1947, with headquarters in Tokyo. The command's original mission was to administer all Navy units assigned to Japan, the Philippines, Marianas Islands, Ryukyu Islands, and Bonin Islands.

In the first three months of the Korean War, COMNAVFE expanded its operating forces from one light cruiser and four destroyers to over 400 ships, many from UN member nations. These ships swept mines, blockaded enemy coasts, conducted surface and air strikes, and transported supplies and troops needed by UN Forces.In December 1952, COMNAVFE moved its staff headquarters from Tokyo to Yokosuka.

In November 1954, operational control of the U.S. SEVENTH Fleet was transferred from COMNAVFE to the Commander, U.S. Pacific Fleet. COMNAVFE retained military command over shore installations, and operational control of Far Eastern amphibious units, and UN and U.S. Navy units charged with the patrol of Korean waters.

In August and September 1954, COMNAVFE provided logistic support for the evacuation of Vietnamese civilians from communist-controlled areas of Indo-China to South Vietnam. In February 1955, assistance was provided in the evacuation of Nationalist Chinese Troops and civilians from the Tachen Islands near China.

In 1957, COMNAVFE was redesignated Commander, Naval Forces Japan. Additionally, the area assigned to Commander, Naval Forces Japan was changed to include only Japan and the Ryukyu Islands.

On February 1, 1962, Commander, Naval Forces Japan was redesignated Commander, U.S. Naval Forces, Japan, as it is known today.

On August 1, 1996, Commander, U.S. Naval Forces, Japan became the immediate reporting senior for all U.S. Naval installation commanders in Japan, as well as the U.S. Navy Support Facility on Diego Garcia, under the Shore Installation Management (SIM) reorganization.

"On 1 October 2003, all U.S. Naval Installation Commanders in Japan and Diego Garcia were realigned under Commander, Navy Region Japan."

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