From his first appointment as Inspector General at the Admiralty, Bentham had a conflict of interest with the Navy Board over the conduct of dockyard business. It was a conflict of ideas, attitudes and loyalties as well as one of practical control. Hostilities erupted openly in 1798 when Henry and John Peake, who had both been appointed to assist the Inspector General, wrote letters to Robert Nelson, second Assistant to the Master Shipwright at Portsmouth, for neglect and misrepresentation of the state of the experimental vessels. Bentham defended them by reflecting on the circumstances of their suspension and trial. Between 1802 and 1804, St Vincent appeared to be using the Commission of naval inquiry to gather evidence against the Navy Board. Bentham offered an alternative ideology and organisation. The threat he posed to the board was enhanced in 1804 when he was permitted to contribute to the building and armament of frigates in the dockyards. Complaints against him strengthened and in 1805 he was sent to Russia, ostensibly to build ships for Britain. In his absence, in 1807 the Commission of naval revision abolished his Admiralty office and transferred him and his staff to work under the Navy Board. Bentham protested vehemently but took his new place in 1808 as Civil Architect and Engineer. His ideas for the construction of the Plymouth Breakwater and a new dockyard at Sheerness were dismissed by the naval officers at the Admiralty Board and in 1812 the new office was abolished.