The head of the Armed Forces has expressed his disquiet over the Royal Navy’s decision to remove from post the commanding officer of Britain’s most powerful aircraft carrier, the Telegraph understands.

General Sir Nick Carter, the Chief of the Defence Staff, is said to be "concerned" over the treatment of Commodore Nick Cooke-Priest amid claims he misused an official car at weekends.

Cdre Cooke-Priest was ignominiously stripped of his command of HMS Queen Elizabeth, the fleet’s newest aircraft carrier, over an allegation that he drove the ship’s Ford Galaxy in his spare time "like it was his own".

The decision to "reassign" the commodore to another role has sparked misgivings at the very top of the Armed Forces, it is understood, with Sir Nick expressing reservations over the handling of the complaint against Cdre Cooke-Priest.

It is understood the Armed Forces head has raised concerns over whether the allegations were properly investigated and whether Cdre Cooke-Priest was provided with proper representation.

There is also a worry that the commodore with a previously unblemished record has been punished too severely for such a minor alleged misdemeanour.