In an open letter, the group expressed "grave concerns that the country does not sleepwalk into a situation that jeopardises its present success in the highly- competitive arena of biomedical research".
The fourteen clinical academics and scientists who signed the letter have vast experience of heading research groups, units and institutes in Scotland, and participating at the "highest level" in the work of grant-giving government agencies, UK research councils and health-related charities.
They argue that Scotland currently does well through its membership of the UK research funding system, and withdrawal from the UK and the creation of a Scottish Research Council would deny the opportunity to win proportionately more grant-funding than Scotland currently contributes.
The Scottish Government has proposed the creation of a common research funding area with the rest of the UK if there is a Yes vote in September.
"Even if this could be negotiated it is highly unlikely that the remaining UK would tolerate a situation in which an independent 'competitor' country won more money than it contributed to drive its research, develop capital projects and infrastructure, and train its research workforce," the academics said.
"We regard creation of a post-independence common research area as an undertaking fraught with difficulty and one that is unlikely to come to fruition."
They added: "In the debate about independence it is ironic that Scottish Government is able to speak freely while the heads of our leading research universities (and the umbrella organisation Universities Scotland) and our premier learned society, the Royal Society of Edinburgh, have to date felt obliged to remain neutral because they receive Scottish Government funding.
"Their silence should not be interpreted as evidence of tacit support for independence on the part of the life sciences research community."
The letter was signed by Professor Dario Alessi, Professor Jean Beggs, Professor Colin Bird, Professor Sir Adrian Bird, Sir David Carter, Professor John Coggins, Professor Richard Cogdell, Professor Sir Philip Cohen, Professor James Garden, Professor Neva Haites, Professor Nicholas Hastie, Professor Wilson Sibbett, Professor Karen Vousden, and Professor Roland Wolf.
A Better Together spokesman said: "This is a serious intervention from people at the very top of their chosen professions.
"They make clear that leaving the UK would have a hugely damaging impact on our world-leading universities and research sector.
"This cannot be dismissed by the nationalists with yet another glib assertion that everything will be alright on the night."
Conservative health spokesman Jackson Carlaw said: "These individuals are among Scotland's most clever and well-intentioned, and they have delivered a thumping blow to the SNP's piffle.
"This is the bleak reality for medical research in the event of separation and it's a bullet the slippery Scottish Government will find impossible to dodge.
"What's absolutely clear is there's a definite link between the quality and availability of treatment patients get, and the amount of money available for research and development."
Professors Bryan MacGregor and Murray Pittock, responding for the pro-independence group Academics for Yes, rejected the conclusions made in the open letter.
They said: "Several bilateral arrangements exist between the UK and the Republic of Ireland.
"These include joint funding arrangements between the UK Arts and Humanities Research Council and the Irish Research Council for Humanities and Social Sciences, the merging of the postgraduate research councils of the Republic and Northern Ireland, and an agreement giving the universities of Ulster and Queen's University Belfast access to the Republic's scientific research funding scheme. Why would an independent Scotland be treated differently?"
They also pointed to what they termed significant current concerns about the UK science funding budget.
They said: "The Campaign for Science and Engineering (CaSE) has noted 'the cumulative erosion' of the science budget of 'over £1.1billion' and CaSE director, Dr Sarah Main, has commented that 'the last four years of a flat cash science budget is biting scientists and engineers and squeezing universities'.
"CaSE also notes that on the proportion of GDP spent on R&D (research and development) 'the UK languishes towards the bottom of the G8 and well below the EU-28 average'.
"In an independent Scotland, policies to develop the R&D base would also benefit universities."