Two of the country's most prestigious academic bodies have raised significant questions over the future of research funding for Scottish universities in the event of a vote for independence.

The Royal Society of Edinburgh and the Royal Society of Chemistry have laid out a range of issues that need to be addressed if the country's science base is to remain competitive, in submissions to the independent Scottish Science Advisory Council.

Scottish universities benefit significantly from research funding from the UK research councils and from major research charities such as the Wellcome Trust.

Scotland has about 8.5% of the UK's population, but wins about 15% of public and charitable research funding.

Scottish institutions won £229 million of research-council funding in 2011/12 and £121m of UK charities' competitive funding in the same year.

The fear is that in an independent Scotland there would be less incentive for English-based research councils and charities to favour Scottish institutions.

In January, UK Universities and Science Minister David Willetts said an independent Scotland would need to find more than £220m in funding for academic research to replace support that it would lose from the UK's seven research councils.

Scottish Science Minister Alasdair Allan had previously suggested an independent Scotland could co-operate with the rest of the UK and continue to pay into a joint research council.

In its submission, the Royal Society asks if the science and engineering base in Scotland could continue to access funding on a UK basis.

"On what basis would the science and engineering base in Scotland continue to access funding from the major research charities and trusts, given that most of them are English registered and operated charities? Would their present constitutions allow this?" the submission asks.

"If these sources of research funding were no longer accessible to Scottish researchers, or only available on a much more restricted basis than at present, what alternative sources of comparable funding could be made available?"

The paper questions if the financial consequences for research funding would affect the ability of Scots institutions to attract and retain outstanding researchers.

The Royal Society of Chemistry added: "If Scotland became independent, would it be feasible to maintain a UK-wide research council framework?

A Scottish Government spokesman said the country had an outstanding record of success in attracting funding that "will continue with independence".

"Our commitment to support our universities and to recognise the full impact of their research is widely recognised in the sector. We fully understand the importance of long-term stability and will set out our plans for higher education in due course."