UK universities minister David Willetts said a Yes vote in September would see Scottish institutions regarded in the same way as those in France or Germany, and therefore no longer part of Research Councils UK (RCUK).
His intervention comes after RCUK’s Professor Paul Boyle told MSPs he hoped the cross-Border network would continue even if Scots back separation.
Prof Boyle told the Scottish Parliament’s education committee on Tuesday that the body “strongly supported” the idea of Scotland remaining part of it.
However, such an arrangement would be without international precedent and would require complex negotiations, he said.
Scottish institutions consistently win 12 per cent or more of RCUK’s total funding, despite the country having about 8.5 per cent of the UK’s population.
Doubts have previously been raised about whether Scotland’s universities could continue to access the funding should the country become independent. Mr Willetts said: “As Prof Boyle pointed out, there is no international precedent where two separate countries maintain a fully integrated research base, such as the current UK system.
“The research councils fund UK-based activities. UK research councils, in the event of a split, would finance research activities in the continuing UK. That is how it would work.
“By and large, we do not finance research activities in France or Germany.
“We would of course collaborate on an international basis wherever possible, but this would not be on the same basis as the current UK-wide arrangements.”
Some of Scotland’s larger universities, including Edinburgh and Glasgow, currently receive up to 40 per cent of their funding from RCUK, which is made up of seven research councils, including the Arts and Humanities Research Council and the Medical Research Council.
Prof Sir Ian Diamond, principal of Aberdeen University and a former chairman of the RCUK executive group, has said there is “no question” Scotland could remain part of the existing network after independence.
A Scottish Government spokeswoman said: “We welcome the UK government’s apparent admission that collaboration with the UK is possible. This comes a day after the head of one of the research councils, representing Research Councils UK – which Scottish taxes already part-fund – confirmed that the current system should remain in place irrespective of the outcome of the referendum.
“We have said that maintaining a common research area with the rest of the UK, including existing shared research councils, is in the interests of both Scotland and the rest of the UK.”