Commodore Nick Cooke-Priest technically remains in charge of the 65,000 tonne future Fleet Flagship but he is no longer on board the warship having been flown off it.
The Royal Navy have taken the decision to remove him as ‘a precautionary measure’ just days after they said that he would sail HMS Queen Elizabeth back to Portsmouth before being ‘reassigned’.
The move comes days after it emerged that he was being sacked after he had used a Royal Naval car for personal journeys.
But a Royal Navy spokesman said on Wednesday: ‘In light of the ongoing investigation, as a precautionary measure to protect both the individual and the Ship's Company, the Royal Navy has decided that Captain Nick Cooke-Priest will not be at sea in HMS Queen Elizabeth.’
It is understood that he nevertheless remains in official command and will formally hand over to the new captain on May 28, as planned.
Suitably qualified personnel are understood to be on board for the passage south.
The decision to sack Cdre Cooke-Priest as captain of HMS Queen Elizabeth has come under heavy criticism since it was revealed over the weekend.
The 65,000-tonne warship is returning to Portsmouth after spending the last six weeks in dry dock at Rosyth in Fife, where it was originally built, to undergo a hull inspection and routine maintenance.
Work carried out during the ship's time out of the water included replacing 284 hull valves, removing and cleaning both rudder blades and applying a fresh coat of anti-foul paint to the ship's bottom.
Successful completion of the work means HMS Queen Elizabeth should not need to dock down again for another six years, the Navy said.
The carrier will go on to conduct a period of sea trials and training before a planned deployment to the east coast of the United States later in the year.