Major engineering interests in Scotland, including the defence contractor Babcock, which runs Rosyth dockyard, have warned that independence poses serious risks to their business.

Babcock issued a short statement confirming that it had told trade unions at Rosyth, where the first of the Royal Navy's two new aircraft carriers is being assembled, that it believed independence carried "additional risks and uncertainties for its business."

The company refused to expand on its short statement but Babcock Marine also runs civil staffing at the Trident submarine base on the Clyde, where its staff are staging strikes in a pay dispute. The base is highly likely to see Trident removed by 2025 if the Scottish National party retain power after a yes vote.

It then emerged that a large majority of Scotland's engineering and electronics firms believe independence "would not be in the interests" of their industry, according to survey by the umbrella organisation Scottish Engineering.

The organisation, which has about 400 engineering, electronics and shipbuilding firms employing between 40 and 2,500 people, said it found only a small minority of engineering companies backed independence, with some reserving judgement until they had more information.

The findings of the anonymous survey came as three engineering unions at Rosyth said Babcock had also warned that the MoD would cancel future military ship-building and refitting contracts at the Fife yard if there was a yes vote in September.

Similar warnings were issued last year about BAE contracts at Scotstoun and Govan on the Clyde, where the Queen Elizabeth-class aircraft carrier hulls are being built.

In a statement to Rosyth workers, the GMB, Unite and Ucatt unions said they believed the yard would be the most likely site for refitting the Royal Navy aircraft carriers if there was a no vote. It was unclear, they added, whether the Scottish government's plans to make Rosyth a naval base after independence would secure the same number of jobs.

Babcock said Scotland's future was a matter for its voters but added: "As a company with a major footprint in Scotland, the possible changes to Scotland's financial and regulatory environments following a vote for Independence create, in our view, additional risk and uncertainty for our business."

Scottish Engineering said it had asked its members four questions: whether they thought independence would be good for the industry; whether that was a matter for voters and parliament; whether more information was needed on taxation or currency; or whether independence would be bad for their sector.

The organisation refused to release precise numbers of votes but said the number who ticked "would not be in the interests of the manufacturing engineering industry in Scotland' outnumbered the total of all those who chose the other three options.

Bryan Buchan, Scottish Engineering's chief executive, said: "There was a substantial response from our membership. The majority of those responding indicated that, in their opinion, independence would not be in the interests of the manufacturing engineering industry in Scotland."

Keith Brown, the Scottish transport and veterans minister, said jobs at Rosyth would be protected. His government was convinced that the UK government would drop its rules forbidding foreign yards building capital warships after independence; UK ministers have insisted those rules will be upheld after a yes vote.

"We pledge to support shipbuilding and defence jobs in Scotland regardless of the outcome of the referendum - it is a shame that no campaign politicians seem unable to do likewise," Brown said. "Let's not forget that the number of Ministry of Defence civilian workers in Scotland has been cut by almost 60% since 2000 – meaning that a no vote brings huge uncertainty for the industry."