The warning comes in an open letter from 14 of Scotland's most noted professors in biomedicine and life sciences.
The letter says: "Growing out of our profound commitment to Scotland are grave concerns that the country does not sleepwalk into a situation that jeopardises its present success in the highly competitive arena of biomedical research.
"Life-sciences research provides thousands of high-technology jobs. It is now and can undoubtedly remain a cornerstone of the Scottish economy."
It adds: "We contend that Scotland's research interests will be much better served by remaining within the common research area called the United Kingdom."
The group includes renowned geneticist Professor Jean Beggs and Professor Karen Vousden, director of the Beatson's Institute of Cancer Research in Glasgow.
They also question the neutral role of umbrella group Universities Scotland and the Royal Society of Edinburgh (RSE), saying they have felt obliged to stay out of the debate as they get Scottish Government funding.
It adds: "Their silence should not be interpreted as evidence of tacit support for independence on the part of the life-sciences research community."
The letter is the latest salvo in an increasingly bitter battle between academics over the effect of independence. At the heart of the row is the structure of Scottish research funding.
The Scottish Government is the largest source of such cash, with £330 million allocated through the Scottish Funding Council in 2012/13 - a third of the total.
But the second-largest contribution is £240m, which comes from competitively awarded grants from the UK-wide Research Councils. UK-wide charities such as Cancer Research provided research grants in Scotland amounting to £121m in 2011/12.
Two rival groups, Academics Together and Academics for Yes, agree the best way to fund research is through the current structure.
Those who support the Union say it would be destroyed by independence, with no precedent for a funding system operating across international boundaries. They also point out that Scotland currently gets a higher proportion of research funding than it could expect to for its population.
But researchers who support a Yes vote argue a single research fund could be maintained, with Scotland continuing to punch above its weight because of the excellence of its research.
Professors Bryan MacGregor and Murray Pittock, on behalf of Academics for Yes, highlighted bilateral arrangements between the UK and the Republic of Ireland as evidence the structure could be kept.
"A sympathetic government in Scotland has provided short-term protection against the financial policies being imposed on universities in England," they said in a statement. "The real threat to research in Scotland's universities is not independence, but continued participation in the Union."
A Scottish Government spokeswoman said: "Our significant investment in research will be protected and indeed could be incentivised to encourage greater collaboration between universities and the private sector, supporting productivity and sustainable economic growth."
She said independence guaranteed an immigration policy that welcomes international students and research talent from across the world.
A spokeswoman for Universities Scotland said it stayed neutral because of the diversity of views in the university community.
She added: "It is for the people of Scotland to decide and it is for us, as an organisation, to respect that decision and then to secure the best possible outcome for universities under whatever constitutional arrangement is decided."
Professor Alan Alexander, general secretary of the RSE, said: "It is not correct to say that we have remained neutral because we are constrained, or feel constrained, by … government funding. The RSE, as Scotland's national academy, must remain neutral to allow it to enlighten and inform - rather than seek to influence - the debate."
l The independence debate must be conducted in a way that is a model for the world despite its intensity, Alistair Darling, leader of the Better Together campaign, said in a speech at Dundee University last night.