UK Government funding for science and research in Scotland would cease if it became independent and replaced by a potentially less secure international partnership, according to the UK Science Minister.
The coalition Government has launched a "celebration" of the UK's integrated research sector with its latest Scotland analysis paper on independence.
Assets would be divided by negotiation, with international examples suggesting Scotland could make a case for retaining all of its existing research assets, but UK funding to maintain them would stop, according to Science Minister David Willetts.
Scottish Secretary Alistair Carmichael said a "brain drain" was unlikely but that it was hard to quantify the effect independence would have on research jobs.
The Scottish Government dismissed advance excerpts of the paper's claims as "nonsense".
Launching the full publication in Edinburgh, Mr Willetts said: "This is a celebration of something that works. Britain has got a world-class science base where we are second only to America in the quality and impact of the science that we do, which is quite an amazing achievement for a medium-sized economy.
"British science across the UK is great. Edinburgh science is great, Glasgow science is great, all the other ones are as well. Abertay does brilliant stuff in computer games for example.
"If the best you can say is you would strain every sinew to try to keep the same thing as you had pre-independence then the game hardly seems worth the effort. Why not just stick with what you have got, which everyone says is working?"
The paper states that Scotland receives a disproportionate share of UK research funding for its population, amounting to around £180 per head compared with £112 for the UK as a whole.
Mr Carmichael said it was hard to see how an independent Scotland could match this funding without cuts to other departments.
He said: "An IFS assessment says the Scottish Government's projected budget would be £3.4 billion in deficit in the first 12 months. Of course the Scottish Government could match that, but something else would have to go as a consequence."
Unionist science group Academics Together, an arm of the Better Together pro-UK campaign, said the paper was a "powerful analysis" of the UK's "thriving" science and research sector.
But Scottish Education Secretary Mike Russell said: "David Willetts's Project Fear paper has lasted barely a day before being fatally undermined by the universities themselves.
"Universities Scotland point out that the way we conduct research 'transcends all borders'. In other words, today's ridiculous report from Tory David Willetts is irrelevant at best and outright scaremongering at worst."
A Yes Scotland spokesman said: "The Westminster Government's own assessment of the performance of UK research underlines the internationally collaborative nature of it."
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