Ed Davey sounded the warning while in Edinburgh to launch the UK Governmentai??i??s latest Scotland Analysis paper, which focuses on energy issues.
The paper looks in detail at how the United Kingdom can maximise energy investment to support thousands of jobs and keep bills as low as possible.
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The National Institute of Economic and Social Research (NIESR) took the view after looking at the likely share of debt and estimated income facing Scotland following a Yes vote.
The Scottish Government wants to set up an energy fund to ai???safeguardai??? the benefits of oil and gas production as an early priority.
The study, commissioned by the Weir Group, says the countryai??i??s economy ai???could succeedai??? if there is a Yes vote in Septemberai??i??s independence referendum.
But it goes on to warn: ai???The end of the Union would create a number of costs and uncertainties, and fewer, more uncertain benefits, for those businesses so vital to Scotlandai??i??s future prosperity, as it goes its own way.ai???
The leader of the pro-union Better Together campaign said there is ai???security, strength and stabilityai??? for small businesses within the UK.
Speaking ahead of a visit to White House Products, an engineering firm in Inverclyde, Darling said independence would create ai???barriersai??? between Scottish businesses and customers in the rest of the UK.
The deputy prime minister suggested that the landmark Wood Review ai??i?? which is expected to help trigger billions of pounds of new investment in the offshore sector ai??i?? would not have happened if the Conservatives were governing by themselves.
The Liberal Democrat leader made the same claim about the multimillion-pound investment in carbon capture and storage (CCS) at Peterhead, the 5p-a-litre fuel discount on the islands, and the freezing of whisky duty in this monthai??i??s Budget.
John Swinney said new figures will be published in the coming weeks.
He made the commitment during a Conservative-led debate on the Scottish Governmentai??i??s financial projections for the country after a Yes vote in the referendum.
Tories will attempt to press the SNP into downgrading expected income to put it in line with more cautious estimates.
The party points to Scottish Government figures which put oil revenue as high as A?7.9 billion in 2016, which could be the first year of independence. It compares with an estimate of about A?3.2 billion from the Office for Budget Responsibility (OBR), set up by the UK Government.