However, the area was given a low priority in funding, and remained largely a paper organization under overall command of the Yokosuka Naval District.

On 12 June 1895, the nominal headquarters of Naval District 5 was transferred from Muroran to the more sheltered port of Ōminato with Mutsu Bay, although facilities and infrastructure were minimal.

On 19 July 1931, the ship repair facilities at Ōminato caught fire and were largely destroyed, and had to be rebuilt a year later.

The attack on Dutch Harbor in the Aleutian Islands that occurred simultaneously with the Battle of Midway was launched from Ōminato.

American forces landed from the USS Panamint (AGC-13) to accept the surrender of the base from the Imperial Japanese Navy on 9 September 1945.