Margaret Thatcher backed an 'open fire' policy at Faslane after a break-in by anti-nuclear protesters, according to previously secret papers.
The Prime Minister was “utterly horrified” by the security breach in early October 1988.
In response, she ordered a crack-down on what she denounced as “slackness in sensitive matters”.
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She was later informed that armed guards at the base had been told that their rules of engagement had been amended and that they that they could "as a last resort, open fire" if they feared sabotage.
But, humiliatingly, just eight years later there was another break-in after two female peace protesters swam into Faslane.
At that stage the naval base housed the Polaris nuclear submarine programme, the predecessor to the current Trident system.
Classified documents released under the '30 year rule' show that Mrs Thatcher's government was humiliated when three anti-nuclear protesters gained access to the control room of a Polaris submarine, the HMS Repulse, on October 9, 1988.
To board the vessel the group had not only dodged guards but had got around a razor wire perimeter.
Once inside they daubed anti-nuclear graffiti in the control room of the Repulse.
They were arrested along with two other intruders who had managed to make their way into the onshore oil depot.
A official report stated that there had been no risk of a nuclear explosion during the incident.
But the newly released documents show that Charles Powell, the Prime Minister’s policy adviser, warned her: “If this had this been armed terrorists the consequences would have been incalculable”.
He added that it was a "very serious matter indeed".
Mrs Thatcher wrote: “I am utterly horrified. Examples of slackness in sensitive matters keep coming to light. Must have an urgent report. We could all have been put in grave danger.”
In response she received a memo from the Ministry of Defence, which informed her: “The rules of engagement governing the armed guards on the Polaris jetties have been amended, with the agreement of the law officers, to make it clear that they may, as a last resort, open fire to prevent a perceived threat of sabotage not only to nuclear warheads but to the submarine.”
A report also recommended a total of 42 reforms, which it said were necessary to tighten security at the base after the break-in.
A number of senior personnel also faced disciplinary action for alleged negligence as a result of the incident.
But the papers reveal that officials feared a series of court martials could do more harm than good.
The documents reveal warnings that they could lead to “exposure (that) would not only provide opportunities for the anti-nuclear movement, but could also be damaging to security”.
However, the increased security at Faslane failed to keep out another group of protesters, this time wearing wetsuits, in 1996.
Two women from the nearby Faslane Peace Camp, swam across into the base in the middle of the night.
They then climbed aboard HMS Sceptre, another nuclear submarine, and were able to enter the vessel via its main hatch.
Once inside they even had the chance to make a phone call before being arrested by the crew and handed over to police.