Responding to comments by Nigel Whitehead, UK chief executive of BAE, that a decision will be taken by the end of the year on the future of shipyards in Glasgow and Portsmouth, East Renfrew-shire Labour MP Mr Murphy said: "This is worrying for everyone involved.
"There must be clarity from the UK government over the future of these yards and workforces. Scotland has such a proud shipbuilding history and it should be a part of our future as well.
"The Tory government plans are adding to the worries but there is one certainty which is that the SNP proposals would sink Scottish shipbuilding.
"The rest of UK would become a foreign country to Scotland and the UK Royal Navy has not built a warship in a foreign land in living memory.
"The Royal Navy order book keeps Scottish yards afloat but independence would see orders dry up. Thousands of jobs are put at risk by Nationalists' plans."
Earlier, the defence giant BAE confirmed it is considering closing one of its major shipyards in a move that could threaten more than 1000 jobs. Mr Whitehead said a decision was expected by the end of the year.
The futures of its three major bases – one at Portsmouth and two in Glasgow, at Govan and Scotstoun – have been under threat after BAE launched a review of its maritime operations earlier this year.
The blow comes after last month's collapse of the planned mega-merger between BAE and Airbus parent company EADS.
The two groups called time on the tie-up – which would have created the world's biggest defence and aerospace group with 220,000 staff and combined sales of £60 billion – after political hurdles proved insurmountable. A statement by BAE added: "We continue to work closely with the Ministry of Defence to explore all possible options to determine how best to sustain the capability to deliver complex warships in the UK in the future.
"This work is ongoing and we are committed to keeping our employees and trade unions informed as it progresses."
The group employs about 3500 staff across its Glasgow but has been coming under pressure from government spending cuts.