Rosyth dockyard owners Babcock have said contracts would be lost if Scotland votes Yes on September 18.
Trade unions, who earlier this year said Scottish independence would cost jobs at the yard, backed the company as it warned of the risks of breaking up Britain in its end of year results.
But Yes campaigners said Westminster was a threat to Scottish shipbuilding.
On a visit to Rosyth to visit the new Forth crossing under construction, Scottish Transport Minister Keith Brown said the shipbuilding industry would be more viable post-independence.
According to Babcock, as well as the potential for Rosyth missing out on Royal Navy work, its operations at HM Naval Base Clyde would suffer long-term reduction in revenue after a Yes vote.
Babcock said in its report: “If the Scottish independence referendum to be held in September 2014 results in a majority vote in favour of independence, the consequences for the group’s businesses cannot be predicted with certainty.”
Raymond Duguid, who is chairman of the dockyard industrial joint council, said Rosyth faced losing half a century worth of contracts to refit the two Queen Elizabeth class aircraft carriers being assembled at the yard.
“That’s potentially 50 years’ work,” he said. “That’s how long the carriers are expected to be in service. That work will not go to Rosyth if Scotland becomes independent. It will be carried out at a British yard and if we are independent we will not get any more work from the Royal Navy.”
Leader of the Scottish Liberal Democrats Willie Rennie said: “Every worker and anybody else with connections to the dockyard, whether business or family, should be very wary of promises given by the Scottish Government on the yard because they are very flimsy commitments.”
Mr Brown told The Courier: “We believe there will be a much more viable industry to support in Scotland post-independence. I think there are real opportunities with independence.
“I think we’ve seen a lot of stuff get into the media by some of the Better Together campaign which is deigned to instil fear.
“We’ve seen massive downscaling in terms of defence in Scotland. We get a tiny share of the defence procurement budget in Scotland. We contribute around £3.3 billion per year to the UK coffers for defence and we get just over half of that back in terms of spend in Scotland, so I’m pretty sure we can start to see the economy starting to flourish in Scotland.”
A spokesman for Yes Scotland said: “The only threat to shipbuilding in Scotland comes from Westminster on whose watch jobs have been slashed to almost half their 1990 levels.”