The head of the Royal Navy has defended the way in which the service handles allegations of rape and sexual abuse, arguing that independent investigations would take longer and “lead to less good outcomes”.

Admiral Sir Ben Key, the First Sea Lord, last month ordered an inquiry into what he said were “abhorrent” claims of inappropriate behaviour in the submarine service.

Admiral Sir Ben told BBC Radio 4’s Broadcasting House programme on Sunday: “It is absolutely true that, for a long time, our investigation processes were too closely aligned with the chain of command, which could then on occasion be seen as presenting a conflict.

“We have changed it now so that anyone who wishes to raise a formal complaint, the admissibility and the handling of that complaint is immediately taken away from the unit they’re serving in and assessed at the headquarters, and will then be independently investigated.”

But he said those investigating such a complaint have to understand the particulars of life at sea, including the pressures experienced by servicemen and women, so that lessons can be learned.

He told the programme: “I know that there are a number of people claiming at the moment that when they talk about independent investigation, that should be completely outside of the Navy altogether.

“But one of my challenges, or concerns, about that is that, actually, that’s just going to add time – and one of the things we really need to do is to investigate these things much more quickly.”

He added: “I would be really worried that if we were setting ourselves in a completely independent process, we would both slow it down, and actually lead to less good outcomes.”

Announcing the investigation on October 29, Sir Ben said sexual assault and harassment have no place in the Royal Navy, adding that anyone who is found culpable will be held accountable regardless of rank.

He said on Twitter at the time: “I am deeply disturbed to hear of allegations of inappropriate behaviour in the submarine service and I want to reassure our people, and anyone who is reading this, that any activity which falls short of the highest of standards the Royal Navy sets itself is totally unacceptable and not a true reflection of what service life should be.

“These allegations are abhorrent.”

It came after allegations were reported in a national newspaper.

The Daily Mail said submariners compiled a “crush depth rape list” in which women were ranked in the order they should be raped in a catastrophic event, and that women were frequently screamed at, called c**** and hit with clipboards and pens.

Speaking to the newspaper, former lieutenant Sophie Brook, 30, said: “The best thing I ever did was leave the Navy but I worry about the women I left behind. It was just a constant campaign of sexual bullying.”

She told the newspaper she loved the job, but said: “It’s just unfortunate the ‘old boys’ club’ makes it such a hostile and misogynistic place.”

The Mail said Ms Brook left the Navy when she was investigated for sharing in an email sensitive information about her submarine’s movements.

The newspaper said she resigned in January but was formally dismissed in June and handed a suspended prison sentence.

Another whistleblower, who previously served in a senior position in the fleet, told the Mail that women are constantly pestered for sex.

The Ministry of Defence (MoD) says that, while most Royal Navy personnel enjoy rewarding careers, for some, predominantly women, their experience has been affected by inappropriate sexualised behaviour.

It says it accepts that more needs to be done and that it is improving reporting mechanisms for sexual offences.

Earlier this year, the MoD announced a zero-tolerance policy to sexual offences, aligning the Royal Navy, RAF, and Army under one approach to dealing with incidents with the aim of enabling services to better support victims and secure justice for them.