The chief executive of a UK-wide body responsible for funding research at institutions across the UK told MSPs he favoured a continuation of the current model regardless of whether Scotland becomes independent or not.
Professor Paul Boyle, of the Research Councils UK (RCUK), said Scotland benefited from being part of the UK-wide research councils - but stressed the advantages were mutual.
It has been suggested that in the event of a Yes vote, Scotland would cease to be able to participate in the UK-wide research councils - which allocated £298 million to Scotland in 2011/12. The fact Professor Boyle supports the continuation of the current model means negotiations to preserve it following independence are more likely to be successful.
His comments came at an evidence session of the Scottish Parliament's education committee, which is looking at the impact of independence on education.
Professor Boyle added: "Scotland benefits from being part of RCUK and I think the view … is we both benefit from having a strong UK research system. In combination we can do so much more.
"Having large funding organisations allows you to invest in big science, which would be more challenging if there was a separate smaller funding organisation."
The session also heard from two Scottish university principals who dismissed claims the referendum was scaring off talent and investors from Scottish science and research. In fact, the MSPs heard, recruitment has been boosted by the independence debate.
Queen Margaret University principal Petra Wend said Scotland is seen as being "more sympathetic to the value of education", adding: "There have been anecdotes … that Scotland does not attract talent any more from other countries because researchers are worried about the future in terms of the EU and research funding and so on. That does not seem to be the case.
"I've asked around other universities as well and, including my own university, we have attracted really excellent researchers from Ireland and England who made the choice to come to Scotland."
Professor Ferdinand von Prondzynski, principal of Robert Gordon University, said Scottish higher education was "seen as a fairly stable setting" and added: "I would agree there is no evidence, whatever one's view of the referendum might be, that this has had a negative impact on our capacity to employ globally. Not just from [the rest of the UK], because I have certainly noticed no change in recent job application patterns, nor outside of the UK or indeed Europe.
"One possible analysis one could make is that the increasingly global discussions about Scotland's future has created a profile for Scotland, and has made people aware of it which might in some respects actually help."
Last year, the UK Government's Scotland Analysis paper on science and research suggested new regulations and institutions associated with independence would create uncertainties for researchers and investors.
Earlier, the education committee heard calls for the Scottish Government to outline why it believes it will be able to retain fees for English students in the event of independence.
As The Herald reported last week, Universities Scotland, which represents university principals, said ministers had to outline a "robust" legal justification of its position before Scotland became independent.
Students from Scotland are entitled to free tuition at Scottish universities, but students from the rest of the UK are charged fees of up to £9000 a year. Any move to continue charging tuition fees to students from England, Wales and Northern Ireland after independence is expected to face a challenge under European law.