Admiral Sir Ben Key, the First Sea Lord, said sexual assault and harassment has no place in the Royal Navy, adding that anyone who is found culpable will be held accountable regardless of rank.
The Chief of the Naval Staff responded to the allegations personally on Twitter.
He said: “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.
“Sexual assault and harassment has no place in the Royal Navy and will not be tolerated.
“I have directed my senior team to investigate these allegations thoroughly.
“Anyone who is found culpable will be held accountable for their actions regardless of their rank or status,” he said.
The statement from the First Sea Lord comes 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***s 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 sensitive information about her submarine’s movement in an email.
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.
They say they accept that more needs to be done and that they are 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 incidences with the aim of enabling services to better support victims and secure justice for them.