Ms Lamont issued the warning as her party launched a new poster campaign focused on the impact of independence on the industry.
She met trade union leaders on the Clyde, where thousands of shipyard workers are employed.
Ms Lamont said that while the shipbuilding industry in Scotland had "come through really tough times", she insisted: "There is a danger that if we vote Yes in September we won't have a shipbuilding industry any longer, because we're reliant on these defence contracts.
"These jobs are at risk if we vote Yes, people need to understand that, but for the SNP clearly that's a price worth paying."
As well as 3,000 jobs in the industry on the Clyde, Ms Lamont said the sector employed "far more than that" across the rest of Scotland.
She also stressed these were "highly-skilled jobs with real career opportunities" and added: "The folk from the shipyards have shown it's not just about their own jobs, it's about making sure these skilled jobs continue to be available in the future."
She said the shipyard industry relied on work from the UK Ministry of Defence (MoD) and insisted it was "inconceivable contracts for defence work will be let outside the United Kingdom" if Scotland became independent.
"It's irrational to think anything else," Ms Lamont added.
"Scotland has a proud history of shipbuilding and despite the serious challenges the industry has faced over a long period, the skills and expertise of the workforce mean that Scottish shipbuilding has a bright future if it secures the defence contracts planned by the UK Government.
"I know from speaking to the workforce that they believe the only threat to Scotland securing these defence contracts and many years' work for our shipyards is a Yes vote, and the expectation is that this work will be moved to England if we vote to leave the UK.
"This would be devastating for Scotland and for the communities who rely on these jobs, and the Yes campaign has left them with nothing but vague assertions and promises that no-one in the shipbuilding industry takes seriously.
"Alex Salmond and Nicola Sturgeon see the jobs on the Clyde, in Rosyth and all over Scotland as a price worth paying for their dream of separation.
"This campaign will argue that the best future for Scottish jobs and business is one where we work in partnership with our neighbours, not work against them."
Duncan McPhee, Unite union convener at the BAE Scotstoun yard on the Clyde, said the MoD was the yard's "major customer", with it being earmarked to build the new type 26 combat ships for the Royal Navy.
He said the contract could provide some years of work for the yard but claimed: "The Ministry of Defence will not build a complex warship outside of the UK.
"Unless the Scottish Government could replace that work, our industry would be decimated if Scotland became independent.
"We have 3,000 jobs on the Clyde at the moment that would be under immediate threat if there was a Yes vote.
"We're here today because we want to help make the public aware of the implications."
Scottish Secretary Alistair Carmichael also visited Babcock Rosyth, where the Royal Navy's new Queen Elizabeth class aircraft carrier is currently under construction, to listen to workers' concerns about Scottish independence.
Following the meeting, Raymond Duguid, Unite convener at Babcock Rosyth, said: "Our message to the minister was we need facts.
"We need to know what Yes means, what No means, and the workforce of Rosyth deserve those answers.
"We're getting those answers, whether they are palatable or not, from the No side. Unfortunately we're not getting them from the Yes side and that's what we need now.
"Our members need to make an informed decision on September 18.
"We are under no illusion that the UK Navy will not come to Scotland to do refits.
"We are building the carrier at the moment but we are primarily a refit yard and that work will not come to Rosyth, we know that, and the Scottish navy in the white paper is not big enough to sustain Rosyth.
"I would question whether he (Alex Salmond) knows where Rosyth is.
"I believe the CSEU has got a meeting set up with Keith Brown, who we always seem to meet but unfortunately no-one higher up the tree wants to meet with the unions and answer difficult questions.
"If they want people in the defence industry to vote for independence, then they need to tell people in the defence industry what is in it for them."
Mr Carmichael said: "The key messages that I heard today from the workforce and the shop stewards is that they are very concerned that with 86 days to go before decision day on September 18 they have still not been told what the future holds for them in an independent Scotland.
"We know that as part of the UK there is a future for the shipbuilding and defence industries in Scotland.
"It's now for the nationalists to come forward with some certainty to the workforce here and elsewhere.
"We are told that neither Alex Salmond nor Nicola Sturgeon is actually prepared to meet the unions or talk to the workforce.
"I have to say I find that very disappointing, if not massively surprising."
Unionists have demanded that Alex Salmond come up with a "Plan B" on currency after all of the major parties ruled out sharing sterling with an independent Scotland.
But Mr Carmichael would not reveal what the UK Government's "Plan B" is for its nuclear weapons if the SNP removes Trident from the Clyde, insisting that the UK Government will not "pre-negotiate" on independence.
"The position on Trident is pretty clear: for as long as we are part of the UK Trident will remain on the Clyde," he said.
"Both government agreed that there would be no pre-negotation. That was a sensible position which remains the position today.
"It's in the interests of both governments that we should adhere to that.
"The question on currency was not pre-negotation. It was simply the advice of the Permanent Secretary to the Treasury saying that he would never advise a Chancellor of the Exchequor in the future to enter into an arrangement of that sort.
"What you have had is three parties saying what they will do in the future. That's not pre-negotiation, that's parties being honest with voters with their future policy."
SNP Westminster leader and defence spokesman Angus Robertson demanded the "disgraceful anti-independence shipbuilding scare stories must end once and for all".
He said: "The No campaign is looking and sounding desperate as they cling on to Project Fear scare stories which have already been dismissed.
"It is beyond belief that anti-independence politicians claim that shipbuilding on the Clyde and at Rosyth is safe in Westminster's hands.
"This is an industry that in the last 30 years has lost thousands of jobs and been decimated by Westminster government after Westminster government.
"The Clyde has been, is now, and will in the future be the best place to build the new generation of naval ships, and that is coming direct from senior directors at BAE Systems.
"Recently, the head of the BAE Type 26 programme, Geoff Searle, said that the company was only looking at a 'single site' solution to build the next generation of warships, and that all of their planning is 'based on the assumption that we will build at the revamped Scotstoun facility' on the Clyde - and that there is 'no plan B' for the build of Type 26 elsewhere in the United Kingdom' if there is a Yes vote - reflecting the fact that they are ending shipbuilding capacity at Portsmouth.
"In fact as Professor Alf Baird, Professor of maritime business at Napier University, suggests 'the re-introduction of commercial shipbuilding in Scotland will only be achieved through independence.'
"The No campaign have also said thousands of defence jobs would go at Rosyth after a Yes vote for independence, however a senior naval source has said that the aircraft carriers have 'got to be finished' at Rosyth, ensuring 2,000 jobs for years to come.
"Rosyth has a bright future in an independent Scotland - including military procurement and its highly successful record in the global market place in a range of other areas, such as offshore energy and marine services, and Labour should stop scaremongering."
Mr Robertson added: "The UK track record on defence in Scotland is appalling, with a multi-billion-pound defence underspend and the loss of more than 11,000 jobs in the last decade.
"With a Yes vote in September we can start to have a defence policy that meets the needs of Scotland.
"With Scotland's own procurement requirements - as detailed in the white paper - along with continued success in the international market, it is clear that shipbuilding has a bright future in an independent Scotland.
"After generations of closure and decline under Westminster, for the first time we will be able to develop a shipbuilding strategy tailored for Scotland."