The head of the Royal Navy has stepped down over allegations he had a relationship with a female colleague under his command.

Admiral Sir Ben Key, 59, has stepped back from all duties while the Ministry of Defence (MoD) carries out an investigation into his alleged extramarital affair.

A Royal Navy source insisted the relationship was “consensual” but added that it was “disappointing” because Sir Ben, who has served more than 40 years in the Navy, was held in such high regard within the Armed Forces.

Sir Ben, who is married with three children, had previously announced that he would retire as First Sea Lord this summer, despite being considered as a frontrunner to become the next Chief of the Defence Staff.

At the time, a senior Navy source told The Telegraph that the reason Sir Ben was standing down was because “he has stared down the bottom of the barrel and doesn’t like what he sees”.

However, when his abrupt departure was announced earlier this week, defence sources speculated that the reason would not be untoward, with some suggesting he may be suffering from poor health.

The MoD told journalists Sir Ben had stepped away for “private” reasons and refused to comment further.