The Royal Marines are to by cut by 200 men to help the Royal Navy crew its new £6.2bn aircraft carriers.
The head of the Navy struck the deal last week amid fears the Marines faced sharp cuts because of a hole in defence spending.
A shake-up will see 200 posts transferred from the Marines to the Royal Navy as it struggles to find enough sailors to crew the biggest warships Britain has ever had.
The decision was made after senior former officers had warned that axing the Marines would send a message to enemies that "Britain is not interested in defending its interests”.
A senior Whitehall source said half the marine cuts would be to backroom functions such as drivers and admin staff. The source said there would be no redundancies and the overhaul will be carried out by the end of the decade through natural wastage.
Marine commanders had been braced for cuts of up to 2,000 men with the Royal Navy struggling to meet the cost of manning the two new Queen Elizabeth class carriers.
The MoD is also trying to find £10bn worth of "efficiencies" in the defence budget during the next decade.
It is understood several senior Naval commanders argued large numbers of Marines should be sacrificed to bolster sailor numbers in the Royal Navy after decades of cuts.
Naval sources said they have enough sailors to man the first 70,000 ton carrier, HMS Queen Elizabeth, but nowhere near enough to man the second, HMS Prince of Wales. Extra sailors are also needed to man the latest nuclear-powered Astute class attack submarines.
Adml Sir Philip Jones, First Sea Lord, said: “The Royal Marines remain bound in to every part of the Royal Navy’s future, from conducting sophisticated operations from the sea, at a variety of scales and against a range of threats, using our new aircraft carriers as a base, to leading the Service's development of information warfare.
The overhaul will also see 42 Commando switch to being a specialised marine operations unit.
Maj Gen Julian Thompson, who commanded 3 Commando Brigade in the Falklands, last week warned that Britain will no longer "be able to stage another Falklands-style operation" if the Marines faced heavy cuts.
In addition to the Marines, the Navy is also considering cutting the number of amphibious landing craft, as well as decommissioning HMS Ocean, the Navy's flagship, whose primary role is as a helicopter carrier and assault ship.
Maj Gen Thompson said last night: “We just hope that also the amphibious ships are not touched. That’s also part of the equation.”
Maj Gen Robert Magowan, Commandant General Royal Marines, said the corps would “ensure that we remain as relevant tomorrow as we do today.”
HMS Queen Elizabeth had been due to begin trials in the North Sea last month and enter its new home in Portsmouth later in the year.
Late last year senior defence sources disclosed that the Armed Forces had begun secretly preparing for another round of defence cuts despite the 2015 defence review which was supposed to boost funding.
They said there is not now enough money available for the various spending commitments already made and therefore more savings were necessary with “very tough choices” ahead.