Mr Swinney was forced to clarify remarks he made last week concerning communications with the bank after it released a statement in light of his comments.
Speaking last Wednesday, the Finance Secretary said "the Scottish Government has had technical discussions with the Bank of England regarding our proposal for a currency union and we welcome their continued acknowledgement that the Bank will introduce whatever the politicians decide".
The following day, the bank released a statement noting Mr Swinney's comments, and saying: ''To be clear, consistent with its statement in December 2012, the Bank of England has not entered into discussions with representatives of the Scottish Government about proposals for future monetary arrangements in Scotland."
Speaking at Holyrood today, Conservative MSP Murdo Fraser said it was an "unprecedented move" by the bank and called on Mr Swinney to tell the Scottish Parliament if he stood by his remarks.
Mr Swinney said: "Following agreement in March 2012 from Mervyn King and as set out to the Scottish Parliament, a number of technical and factual discussions have taken place with the Bank of England.
"Following the first meeting between the First Minister and Governor Carney in January of this year, it was agreed that the technical discussions inaugurated by his predecessor Lord King between the Scottish Government and the Bank of England in advance of the referendum would continue.
"If by my choice of words last week I have given the impression that the Bank of England has been involved in negotiating a currency union I can say to Parliament that that was not my intention."
Mr Swinney said the "factual and technical discussions" were to inform the work of the Scottish Government's Fiscal Commission Working Group, set up to develop an economic framework for an independent Scotland.