The Royal Navy said the decision surrounding Commodore Nick Cooke-Priest has been taken as "a precautionary measure".
The commodore was flown off the ship as it was anchored in the Firth of Forth.
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 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.