Companies such as RBS, Lloyds, BAE Systems and Diageo are among those who could experience an "adverse reaction" to a Yes vote, it states.
The report by Barclays, Scottish Independence: Implications for Equities, considers the potential implications of independence for publicly-listed companies.
It states: "A Yes vote in support of Scottish independence on September 18 could have a modestly negative impact on the UK stock market."
The report notes that "independence would present several companies with significant challenges", but it also acknowledges potential benefits for other firms.
"Our analysis points to 10 key areas of potential impact for companies, ranging from the likely currency regime to pensions, labour cost, taxation and procurement. We then go on to analyse how these could affect major sectors," it says.
"To do this we have undertaken a comprehensive review of public statements by key industry leaders and combined them with the assessments of our own analysts."
It adds: "On balance, our work shows that a "yes" vote could have significant consequences for stocks in the banks, oil, defence, beverage, transport, business services, asset management, insurance, utility, property and industrial sectors.
"More precisely, based upon companies' public statements and our analysts' assessments, we have identified the following stocks with potential for an adverse reaction to a "yes" vote: BG Group, Wood Group, RBS, Lloyds, Diageo, BAE Systems, Babcock, SSE, Aggreko, Weir Group and Standard Life."
"On the other hand, the following companies could experience a beneficial impact from Scottish independence: easyJet, Ryanair and IAG, as a result of the Scottish Government's commitment to halve air passenger duty, and London-based property companies such as Derwent, Great Portland Estates, and Berkeley Group."
A spokesman for Scotland's Finance Secretary, John Swinney, said: "Scotland is one of the wealthiest countries in the world - more prosperous per head than France, Japan and the UK itself - but we need the powers of independence to make the most of our huge resources, for example by encouraging tourism and trade through lowering Air Passenger Duty.
"An independent Scotland will be a hugely attractive place to do business and to invest in, which is just one of the reasons why a currency union will be agreed."