The unit, known as the Commachios, is made up of nearly 500 Royal Marines.
The move follows a series of security scares at the Clyde base - including its infiltration by a car load of lost pensioners.
The Fleet Marine Protection Group will be moving into new headquarters at the Trident base in April.
The unit, known as the Commachios, is made up of nearly 500 Royal Marines.
The Commachios are said to be an unofficial part of the Special Boat Squadron, the Royal Navy's equivalent of the SAS.
A spokeswoman for the base said: "They are relocating their headquarters to the naval base next April.
"Their job is to guard the base and that is what they will be doing."
Investigation launched
Peace protesters have repeatedly evaded security at Faslane and been arrested deep within its perimeter.
And an investigation was launched last month after pensioners "infiltrated" the Clyde base.
The driver of the car reportedly asked security guards who eventually stopped him inside the base if he was on the road to Arrochar.
A security guard was suspended pending an inquiry into the incident.
"There is no suggestion that there was any criminal intent, but it was a
breach of security and therefore it is treated very seriously," a spokesman said at the time.
Anti-Trident activists have cut through fences, climbed over barbed-wire barricades and come within yards of the submarines.
Last year, a landmark ruling at Greenock Sheriff Court cleared three women of deliberately damaging research equipment at a facility related to Faslane on the grounds they were "disarming" the nuclear deterrent.
Sheriff Margaret Gimblett ruled that the use of the deterrent was illegal.
Ruling challenged
The women told how they had used a leaky inflatable boat to get on to a barge used for research at the base.
"We had time to have a picnic before we were arrested. We had sandwiches and grapes," said Ellen Moxley, one of the three women.
The Crown has mounted a challenge to that ruling, asking three judges to rule that Britain's nuclear arsenal is legal.