The submarine's captain and his second-in-command are the only officers on board with access to a grey safe which contains a 'letter of last resort' from the Prime Minister. It details guidance and orders to be followed should the UK be attacked with nuclear weapons.
Meanwhile, another serviceman on the vessel faces court martial after going AWOL - absent without leave - and boarding a flight to the UK to see his girlfriend. Two more submariners have quit the boat in the wake of the scandals.
It means that around 10 per cent of HMS Vigilant's 168-strong crew have either been kicked out, quit, are under investigation or have been removed in what is believed to be one of the biggest sex and drugs scandals to hit the Navy.
The matter is so serious that the First Sea Lord, Admiral Sir Philip Jones, has been quizzed about the scandal by the Defence Secretary, Sir Michael Fallon, who is said to be "furious".
It is understood Sir Philip has been ordered to force mandatory drug tests across the entire submarine fleet to "reassure the Defence Secretary that this was an isolated incident". A major investigation is also under way in the Ministry of Defence.
HMS Vigilant is one of Britain's four Vanguard-class submarines which carry up to eight Trident missiles armed with nuclear warheads.
Britain has had a continuous at-sea nuclear deterrent since 1969. At least one of the four submarines is always supposed to be on patrol at any given time.
The fact that such a serious scandal could unfold on board one of these vessels is likely to cause considerable alarm.
It will also raise questions over whether men and women should be allowed to serve together under water for such long periods.
Women have served on Navy surface ships since 1990 but a ban on them serving on submarines was not overturned until 2011. The first female submariners started work three years ago.
Last night, a Navy source said: 'These guys had been under the sea for 91 days - what do you think is going to happen? It was a month-long party and it should not have been happening. HMS Vigilant has become known as the party boat.'
Rear Admiral Chris Parry, former commander of a Type 42 destroyer, said: 'This is not just a submarine, it is one of our deterrence submarines. It is absolutely disgraceful. People in the Navy should remember playing for our country on an international level is a great privilege. It is a question of putting service before self.
"Duty is everything. As Lord Nelson said, "Duty is the great business of a sea officer, all private considerations must give way to it"."
Within the chain of command, relationships are banned. Where relationships exist in a crew outside the command chain a strict 'no touching' policy is in place while on deployment.
The scandal erupted when the submarine sailed to Kings Bay, Georgia, in the US in September. Senior naval chiefs were dispatched to the nuclear submarine after a whistleblower at the vessel's Faslane base reported concerns about two affairs.
Once it docked, officers were put up in a £100-a-night hotel in Florida and junior and senior submariners were put up in a cheaper hotel. They were in-between the hotels and the submarine for a month while work was carried out on the boat.
Junior sailors first knew something was wrong when they were ordered by senior officers to delete all of their social media accounts.
They were then told to get back on the submarine for a meeting, where they were told the captain had been removed.
A few days later Lieutenant Commander Seal was taken off, with Lieutenant Edwards and Lieutenant Litchfield, for questioning.
While the investigation into the alleged affairs was ongoing, junior and senior rates had drug-fuelled parties in their hotel and one man cavorted with prostitutes in the swimming pool, it is claimed. Senior officers got wind of the parties and ordered a drugs test before the crew were let back on board.
Nine of the junior rates failed the test. Four of them were flown home immediately before being kicked out of the Navy in recent weeks.
A further five were also sent home during an investigation and were kicked out yesterday.
Days before HMS Vigilant left the US, one of the submariners decided he had had enough and flew back home to see his girlfriend. He was arrested several hours after arriving in the UK and now faces court marital for going AWOL.
Two sailors also quit after details of the affairs emerged and after they were told some of their leave would be cancelled next year.
Five officers threatened to quit over the scandal, although it is understood no officers actually handed in their notice. The crew on the boat was around 168-strong, including seven women.
Last night, a Navy spokesman said: "We do not tolerate the misuse of drugs by service personnel. Those found to have fallen short of our high standards face being discharged from service."
The spokesman confirmed an investigation was underway.
Revealed, the Navy girl in a fling with No2
The identity of the female Navy officer in her 20s at the centre of a nuclear submarine sex scandal can be revealed today.
Lieutenant Hannah Litchfield, 27, an engineering officer on HMS Vigilant, is believed to have had an 'inappropriate relationship' with the boat's second-in-command.
Married Lieutenant Commander Michael Seal, 36, was last month hauled off the Vanguard-class submarine, which carries Trident missiles, amid accusations he was having a liaison with a subordinate.
He was removed from the boat after it docked in the US just days after the captain was taken off amid claims he too was in a relationship with a female junior officer.
The captain and second-in-command are the only officers to have their own rooms.
As the more senior officers, the men are expected to face a greater punishment than the women should they be found to have breached the Navy's social conduct regulations.
Relationships within the chain of command are banned and where relationships exist in a crew but outside the command chain a strict "no touching" policy is in place.
Both women were quizzed about the allegations after a whistleblower at the vessel's Faslane base reported concerns about two affairs. The men were taken off the boat and relieved of their duties while the investigation is ongoing.
The women were able to continue their work while the investigation is carried out, although they are no longer on the boat because they were due to finish the deployment anyway.
Father-of-two Lieutenant Commander Seal is married to Jennifer, 36, who lives at their family home in Kirkcaldy, Fife.
A Royal Navy spokesman said: 'We can confirm an investigation is underway, but it would be inappropriate to comment further at this stage.
"Any allegations of wrongdoing are taken very seriously and will be dealt with appropriately."
