The Treasury's conclusion to reject a formal currency union is based on incomplete evidence and took no account of work already conducted for the Scottish Government, John Swinney said.
He responded hours after Chancellor George Osborne, with support from Labour and the Liberal Democrats, ruled out the SNP's preferred option for an independent Scotland.
"The Chancellor made clear his conclusions on currency union were based on the advice of Treasury officials," he said.
"That advice is incomplete and with regard to the size of the Scottish financial sector and operation of monetary unions is backward-looking and takes no account of the comprehensive evidence provided by the independent economic experts of the fiscal commission, including two Nobel laureates, Professor James Mirrlees and Professor Joseph Stiglitz.
"On every one of the four points the Chancellor rehearsed, the fiscal commission working group have already published comprehensive advice and their proposed macroeconomic framework is a workable model that would ensure financial stability and allow both governments autonomy over economic and social policies, including fiscal policy. The governor of the Bank of England has confirmed the Bank will deliver a currency union if agreed by both governments."
Mr Swinney rejected Mr Osborne's claim that Scotland would not be able to enjoy full economic freedom while in a currency union. And he insisted the opportunity to change currency arrangements should not be a barrier.
Mr Swinney said: "All sovereign states have the ability to determine currency arrangements that are appropriate for their circumstances. That is not a barrier to successful currency unions."