Defence giant BAE Systems has announced that 1,775 jobs are to go across its three shipyards.
In addition, the firm will end an 800-year-old tradition of shipbuilding at Portsmouth with 940 jobs to go there by the second half of 2014, reducing the 1,200 workforce to just 260.
A further 835 are going to go at Scotstoun and Govan shipyards in Glasgow, Rosyth, and Filton, near Bristol.
The cuts are part of a maritime defence review, which BAE systems launched 18 months ago.
A statement from BAE said: "(The) company proposes to consolidate its shipbuilding operations in Glasgow with investments in facilities to create a world-class capability, positioning it to deliver an affordable Type 26 programme for the Royal Navy.
"Under these proposals, shipbuilding operations at Portsmouth will cease in the second half of 2014."
Confirming the announcement in a statement to the House of Commons the Defence Secretary, Philip Hammond, said that the losses were "regrettable but inevitable".
He said that the shipyards would have been unable to sustain such a large workforce once the £6.2bn project to build the Royal Navy's largest ever aircraft carriers came to an end.
The decision has taken on significant political prominence with the Scottish referendum looming in 2014 and warnings any closure of one of the Scottish yards rather than Portsmouth would have handed First Minister Alex Salmond "a victory on a plate".
It has led to claims that Portsmouth jobs have been sacrificed to save the BAE shipyards at Govan and Scotstoun.
Mike Hancock, independent MP for Portsmouth South, said: "I think personally it is a real tragedy for them as individuals and for us as a community in Portsmouth.
"To lose close to 1,000 jobs in this way is a bitter blow. There has to be some element of cynicism being brought into play here to suggest this is simply being done to suit the financial situation at BAE and the Scottish referendum must have played some part, albeit maybe a small part.
"I think people would be foolish not to think that that was something in the background."
Ending shipbuilding at Portsmouth would mean the UK would lose the ability to build its own warships if Scotland is granted independence in 2014.
Gerald Vernon-Jackson, leader of Portsmouth Council, said: "I condemn the decision to shut down the last remaining shipyard in England with the capability to build advanced surface warships.
"This decision is bad for Portsmouth, with the loss of many highly skilled jobs, but it's also bad for the defence of the UK and for the Royal Navy.
"The remaining yards with the capability to build advanced warships are in Scotland, and the referendum on Scottish independence is less than one year away. Ministers have put the defence of the UK and the future of the navy at real risk."
Asked about the decision, the Prime Minister's official spokesman said: "This is a Government that always takes decisions based on the national interest.
"This decision was taken with a view of how we have the best-equipped, best-maintained Royal Navy. That is the basis on which it was taken."
Mr Hammond also announced that the Ministry of Defence would be giving BAE the contract to build three Offshore Patrol Vehicles to bridge the gap between the aircraft carrier project ending and the beginning of work on the new Type 26 warship in 2016.
This, he said, was to avoid having shipyards being paid to lay idle, with workers losing valuable skills.
He said that Portsmouth dockyard would continue to do repair and maintenance work.
Unite national officer for shipbuilding Ian Waddell said: "This is a very worrying time for the workforces and their families as the work on the two carriers comes to a conclusion.
"Unite will be working very hard to retain the maximum number of jobs at both Portsmouth and in Scotland.
"It is a huge blow to Britain's manufacturing and industrial base, with many highly skilled workers faced with losing their jobs."