The notion of using naval rather than merchant vessels as troop ships was the subject of considerable debate throughout the wars. Though there were strong arguments that supported this in terms of flexibility, reliability and security, the Admiralty objected vociferously. It was adamant that there were not enough naval vessels that might be converted for such purposes. Furthermore, it claimed that to custom-build a fleet of troop ships would be cost-prohibitive and would take up valuable shipbuilding capacity. The professed insufficiency of ships was questionable. There appears to have been a considerable number of ships in ordinary which might well have been suitable. However, the more realistic obstacle was the limited availability of seamen. There were never enough experienced seamen to fulfil the operational demands of the navy.

The Admiralty's overriding concern related to the precedence of authority when troops were on board naval vessels, and this issue compounded its reluctance to supply troop ships. Indeed there had been open dispute between naval and army officers about whose authority troops on board naval vessels should observe. When, in 1794, Henry Dundas, Secretary of State for War, applied to the Admiralty for three 44-gun ships to transport troops, Lord Chatham, the First Lord of the Admiralty, refused to comply unless it was clearly understood that the soldiers would be subject to naval command whilst on board: ‘It was several weeks before this delicate issue of inter-service relations could be sorted out to the Admiralty's satisfaction.’

Then, in 1795, when the navy court martialled an army lieutenant serving as a marine in the Mediterranean fleet for insubordination, the army commander in the Mediterranean refused to recognise the court martial and ordered the lieutenant to rejoin his regiment. The case was referred to London where government law officers eventually endorsed the court martial verdict. This worsened relations between the two services, and to avoid a reoccurrence the Duke of York, Commander-in-Chief of the army, established regulations empowering naval officers to arrest and detain soldiers only until they could be court martialled by the army.