Several "larger PLCs" would move their headquarters south of the Border as soon as they felt the "direction of travel" in separation negotiations would hurt the pound or put up barriers to trading, the Edinburgh University study found.
It is one of a number of findings from the research, with most business leaders interviewed nervous about constitutional change. This also included additional devolution or a UK exit from the EU.
Brad Mackay, a professor at Edinburgh University's Business School who led the study under the auspices of the independent Economic and Social Research Council's Future of UK and Scotland project, stressed bigger firms, those with cross-border interests, had the biggest jitters.
In a report summing up his findings, he said: "The decisions that these firms take will depend, not on the outcome of the negotiations, but on their direction of travel.
"If it looks like a currency union is unlikely, for instance, or that independence will create any trading barriers between Scotland and its biggest market, England, it is likely that several headquarters of the larger PLC companies will be moved out of Scotland.
"The prospect of independence poses a particular challenge for the majority of businesses in Scotland because of the nature of the Scottish economy, which is highly integrated with, and dependent on, the wider rUK economy."
Mr Mackay and his team talked to more than 70 executives in companies of different sizes from a variety of industries, including food and drink, manufacturing and life sciences. One business leader said he or she believed HQs would be lost after independence. "Why would I want to base myself in a market of five million when there's a domestic market of 58m on my doorstep?"
This week 200 prominent business voices, including Jim McColl of engineering group Clyde Blowers, came out for Yes.
Another 130 industry leaders signed an open letter backing No, although Better Together claimed yet another 100 would have done so but were afraid of a "Nationalist backlash". It provided no evidence for this.
Mr Mackay's qualitative study allowed business leaders to make their positions clear anonymously. He stressed a post-referendum deal on the pound and other issues might placate them.
He said: "If the sort of wide-ranging partnership that the Scottish Government is advocating with the rUK was to materialise, some of the drop in private sector economic output that we can expect from a Yes vote might be mitigated."
However, businesses, he said, were not just worried about the risks of Yes.
He said: "Of course, a 'no' vote also brings with it uncertainty, particularly over what further powers might be devolved to Scotland (and whether such powers might create divergence between Scotland and the rUK in terms of tax policy and the fiscal regime), whether such powers might be devolved at all, and the possibility of a UK in/out referendum on the EU depending on the outcome from the 2015 general election." He also found smaller firms, and large international companies, were more relaxed about independence.
Tony Banks of Business for Scotland, a pro-independence group, stressed not all feedback in the report was negative.
He said: "The company executive who said 'I don't see any risks at all, I see only opportunity' sums it up for me. A fresh approach to exports offers us the chance to improve our already impressive exporting record. Scotland is a net exporter with a positive balance of trade while the UK is a net importer with a negative balance of trade.
"That was mirrored by the concerns expressed over a No vote with the uncertainty it would bring and Tories winning another term and dragging us out of the EU. That's the big threat to Scottish business: a No vote and a European exit."
Mr Mackay's report revealed that half of businesses interviewed were able to think of an opportunity from independence - a fact welcomed by Mr Banks - but only a tiny minority saw the change bringing prospects for investment.
The SNP's flagship corporation tax cut policy did not excite them. "I don't think you are going to change jurisdiction for a couple of percentage points here or there," said one food and drink business. Financial services firms, according to Mr Mackay's interviews, were particularly worried - about currency and regulation.
This chimed with another report published yesterday, by Capital Economics, predicting "wholesale relocation" of financial services after independence. The research firm believes stock and debt markets are expecting a No vote but warned there would be a "strong market reaction" if here was a Yes.
Uncertainty, they said, could lead to a stronger sell-off of Scottish equities and "significant withdrawals" from Scottish banks. The report said: "We would not be surprised if the Bank of England's contingency preparations included capital controls to prevent a run on Scottish banks immediately after the referendum."