The Navy captain removed from command of HMS Queen Elizabeth is understood to have allowed his wife to use the ship's car, and it has emerged he was reported by his own crew.

Commodore Nick Cooke-Priest was stripped of his command of the fleet's newest aircraft carrier over a claim that he treated the Ford Galaxy "like it was his own".

However, his dismissal turned into farce when it was announced that he would still take the helm of the ship to sail from Rosyth to Portsmouth, only for that decision to be quickly reversed by the Royal Navy and the captain flown off the ship.

The Telegraph now understands that Cdre Cooke-Priest is believed to have allowed his wife to use the vehicle for personal trips including the school run.

One source alleged that the outgoing Commanding Officer of Britain’s £3 billion aircraft carrier had let his wife use the car when HMS Queen Elizabeth was at sea.

Senior Defence sources have told the Telegraph that Cdre Cooke-Priest had been warned on more than one occasion over the inappropriate use of the ship’s Ford Galaxy.

The Telegraph understands it was the discrepancies between the vehicle worksheet, documenting who used the vehicle, for what purpose and for how long, and the recorded mileage on the car that first alerted authorities.

It is believed that members of Cdre Cooke-Priest’s own crew would have highlighted the inaccuracies.

View photos The Prince of Wales with Captain Nick Cooke-Priest Credit: PA More

The driver of the vehicle is only insured once the official worksheet is signed, raising questions over whether adequate insurance cover was in place for any alleged trips made by Cdre Cooke Priest’s wife.

A senior Navy source said: “Everyone knows the rules; it’s not as if you stumble into them when you become Captain. It’s how we are governed as public servants.”

When Cdre Cooke-Priest was first "reassigned" from command of HMS Queen Elizabeth it was reported that he had never been warned that using the Ford Galaxy for personal journeys was in breach of rules. He is understood to have paid for his own petrol and there is no allegation of fraud.

Former commander of Joint Forces Command General Sir Richard Barrons said that given the nature of the allegations, removing Cdre Cooke-Priest from the ship was the right decision. He said: “This is the Queen Elizabeth, not a Minesweeper - no offence. It’s iconic.

“The Commanding Officer is the overseer of probity among the crew. If it became well known that he had broken the rules then he couldn’t claim to be leading by example and his authority over the crew is diminished.

“If the Commanding Officer’s position is seen as shaky to untenable, the kindest thing is to sort it out.”

The reversal of the decision to allow Cdre Cooke-Priest to bring HMS Queen Elizabeth back to Portsmouth was met with surprise on Thursday. The initial decision was taken on the basis he had been “reassigned” to other duties, rather than sacked, and remained in command of the ship.

View photos Commodore Nick Cooke-Priest has been stripped of his command Credit: PA More

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