Commissioners for Transport, whose main responsibility was the transport of troops overseas, were first appointed in 1686, were abolished in 1687, revived in 1688 and abolished again in 1724. In 1794 the Transport Board was re-formed; in 1796 it took over responsibility for prisoners of war from the Sick and Hurt Board. The Transport Board (after some initial confusion) kept the business of prisoners in a separate series of records from those of the transport service.In 1806 the Sick and Hurt Board was abolished and the naval medical service entrusted likewise to the Transport Board.
Some of the former Commissioners for Sick and Wounded Seamen joined the Transport Board and formed a Medical Committee, which administered medical affairs without interference from the Transport Board proper. The Transport Office now maintained three series of records for its three responsibilities.
In 1817 the Transport Board was itself abolished, its duties being divided between the Navy Board, which set up its own Transport Branch, and the Victualling Board, which took over the medical commissioner as well as setting up its own transport organisation.
A Transport Account Committee, presided over by one of the former Transport Commissioners, continued until 1818 clearing up the residual business of the Board. The remaining business of the Prisoner-of-War Department was attached to the Medical Department (now under the Victualling Office), which continued as before to be administered by a semi-autonomous Medical Committee.
When the Navy and Victualling Boards were abolished in 1832 transport duties were assigned to the Comptroller of Victualling and Transport Services, but in 1862 that office was divided and a separate Director of Transports appointed. He was responsible, under the superintendence of the Fourth Sea Lord, for transporting troops and seamen and Navy and Army stores.
In March 1917 the Transport Department was incorporated in the Ministry of Shipping and subsequently in April 1921 its functions were transferred to the Mercantile Marine Department of the Board of Trade, although the Fourth Sea Lord continued to have an interest in the planning and operations of the Transport Service, and especially during the Second World War under the Ministry of War Transport.