The Navy is now under pressure to conduct a full investigation into its handling of the case.
The Telegraph disclosed further embarrassment for the Navy yesterday when it emerged that Cdre Cooke-Priest had had to be recalled to take temporary charge of the ship.
Naval chiefs realised there was no one available to take the helm in bringing the £3billion ship back to her home on the south coast.
A family friend of the 50-year-old commodore said he had been “flown to Rosyth to sail the ship back to Portsmouth”. Cdre Cooke-Priest, who joined the Navy in 1990, had been in charge of HMS Queen Elizabeth since October.
It is understood he was found to have been guilty of an “error of judgment” in using the Ford galaxy for private journeys although he had paid for the petrol himself and there is no allegation of fraud.
Cdre Cooke-Priest will be replaced on may 28 by Captain Steve Moorhouse, the current commanding officer of HMS Prince of Wales, a second aircraft carrier due for commissioning in 2020.
Penny Mordaunt, the Defence Secretary, said she understood the ‘concern when we have invested in an individual and they are not able to carry out the tasks for which he was trained”.
But Ms Mordaunt insisted the matter was “for the Royal Navy to deal with”.