Ian Davidson, Labour chairman of the House of Commons Scottish Affairs Committee, said the choice for Scottish shipbuilding was clear: stay in the UK and have a secure source of work for decades, or leave and see orders from the UK dry up.
There is fresh speculation that BAE Systems, which operates two shipyards and employs 3500 people in Glasgow, will wind down Scottish operations.
Angus Robertson, the SNPs' leader at Westminster, insisted the committee's claims were not supported by the facts. He said evidence from Vice-Admiral Andrew Mathews – omitted from the committee's report – confirmed the UK Government would keep the option to build Royal Navy vessels on the Clyde if Scotland became independent.
He said the report was also at odds with a recent Ministry of Defence disclosure that businesses in Scotland had received only 5.3% of defence contracts exempt from EU legislation, which represented an underspend of £1.8 billion during the last five years compared to Scotland's population.
"This is a shoddy and partisan report from Ian Davidson, which brings the Westminster system into disrepute," Mr Robertson said. "It is not only unsupported by facts but ignores the actual evidence provided to the committee."
"This Labour-led committee's primary job is to scrutinise the UK Tory-led government but it has shown itself to be nothing more than an extension of the Tory/Labour anti-independence campaign." Nationalists do not attend the committee, because of a dispute.
The SNP defence spokesman accused Mr Davidson of "airbrushing" the evidence from Vice-Admiral Mathews.
Meanwhile, BAE Systems dismissed reports it will close its Portsmouth shipyard, run down some operations in Glasgow, and cut thousands of jobs.
A spokeswoman said: "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."
An announcement on BAE's rationalisation is expected in the next few weeks.