The bank said that there had been no such talks and that it had done no more than answer technical questions from the Scottish Government.
In an unusually blunt statement, it said: "The Bank of England has not entered into discussions with representatives of the Scottish Government about proposals for future monetary arrangements in Scotland".
Earlier this week Mr Swinney said that Scottish ministers had had "technical discussions with the Bank of England regarding our proposal for a currency union".
His comments came after the Governor of the bank, Mark Carney, announced it was drawing up contingency plans for a potential Yes vote, following warnings the result could trigger a run on the banks. Last night the Scottish Government insisted that Mr Carney himself had admitted last February that such technical discussion had taken place.
At that stage the bank said it "stood ready" to provide "technical assistance to advisers to the Scottish Government's fiscal commission" looking at the issue.
Scottish Conservative leader Ruth Davidson MSP said that the SNP's "spinning" had unravelled "within 24 hours". She said: "It is utterly embarrassing that Scotland's Finance Secretary has had to be slapped down by the Bank in this humiliating manner."
Meanwhile, the Tory LibDem Government distanced itself from Mr Carney yesterday insisting it was making no plans for a Yes vote.
Announcing the contingency plans, Mr Carney said: "Some of the things, some of the powers we have are held jointly with Her Majesty's Treasury ... we are not the sole decision-maker in these areas."
Pro-independence campaigners Business for Scotland said Mr Carney's comments had blown out of the water claims no preparations were being made for a Yes vote. A Scottish Government spokesman said: "The Scottish Government has had ongoing technical discussions with the Bank of England, as the Bank itself has previously confirmed.
"These technical discussions were inaugurated by former Governor Mervyn King and continued under the current Governor Mark Carney, as confirmed in the statement issued after the meeting between the First Minister and Mr Carney on January 29th this year, which was agreed by the Bank.
"We have always made clear that these are technical discussions and not negotiations, and that we respect the neutrality and independence of the Bank, which had made clear it will implement whatever is agreed."