When established, the Bureau of Navigation was a part of the United States Department of the Treasury.

In 1903, the organization was transferred to the newly formed United States Department of Commerce and Labor.

[3] In 1942, Executive Order 9083 transferred many functions of the bureau to two other agencies: Merchant vessel documentation was transferred to the United States Customs Service, while functions relating to merchant vessel inspection, safety of life at sea, and merchant mariners were transferred to the United States Coast Guard.

[4] The merchant vessel documentation functions were also transferred to the Coast Guard in 1946.

With all its functions having been absorbed by the U.S. Customs Service and the U.S. Coast Guard, the Bureau of Marine Inspection and Navigation was abolished as unnecessary and redundant by Reorganization Plan No.