Danny Alexander has said an independent Scotland's economy would face a £4 billion black hole the year the SNP hope to break from the UK.
Mr Alexander said the figure reflected forecasts of falling oil revenues, while Coalition sources suggested it could be even higher in subsequent years.
However, the SNP accused the Chief Secretary to the Treasury of treating oil revenues as a form of short-term cash cow.
The row comes just days before the latest figures are expected to show Scotland was in surplus last year.
The figures, which include a geographical share of North Sea revenue, are contained in the annual Government Expenditure and Revenue Scotland (Gers) report. The Treasury concedes that last year was very good for oil revenues.
The calculations of an economic black hole are based on figures produced by the independent Office for Budget (OBR) Responsibility last year.
At that stage the OBR said it had dramatically slashed its forecasts, blaming falling production, higher expenditure and lower oil and gas prices.
In a speech to the Aberdeen Chambers of Commerce, Mr Alexander said: "Of course, with where the oil price and production levels have been the last couple of years, the Gers figures published next week may well look favourable. But the volatility of price and production cannot be wished away.
"By 2016-17 – the Scottish Government's preferred year to begin independence – it is forecast revenues will be half the average of recent years."
The SNP accused Mr Alexander of selective amnesia over 2010's £10bn tax raid on North Sea profits. A study released last week showed that only this year had investment in the sector recovered after the move, which came as a shock to oil producers.
A spokesman for Finance Secretary John Swinney said: "Scotland already more than pays its way in the UK, as the figures show and as Danny Alexander has been forced to admit.
"In 2010-11, Scotland's surplus relative to the UK was equivalent to around £500 for every man, woman and child in Scotland, and as an independent country we will be able to use all of our huge resources to create a wealthier and fairer society."
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