The Deputy First Minister said he had misheard the question after claiming the SNP would have a mandate to start independence negotiations with the UK if the party won a majority of MPs north of the border at the next general election.
It comes after Nicola Sturgeon unveiled plans to hold a second referendum on October 19, 2023.
The First Minister said judges at the UK Supreme Court were being asked to consider whether Holyrood could legislate for a referendum without the support of UK ministers.
If that ballot cannot take place, she said the next Westminster election would be a “de-facto referendum” on Scotland’s place in the UK.
Mr Swinney was pressed on the issue on BBC Radio Scotland’s Good Morning Scotland, where he was asked if winning a majority of Scottish MPs at the next UK election would give the SNP a mandate to start negotiations for independence.
He replied: “That’s correct, yes.”
This was later contradicted by Ms Sturgeon, who said independence could only happen if "a majority of people vote for that proposition".
This would require the SNP to achieve a Scottish vote share of more than 50 per cent at the next general election – a much bigger hurdle than simply securing the most MPs.
Mr Swinney said he had misheard the question, tweeting: “Referenda, including de-facto referenda at a UK general election, are won with a majority of votes. Nothing else.”
Pamela Nash, chief executive of pro-UK campaign group Scotland in Union, said: “It took less than 24 hours for Nicola Sturgeon’s plan to plunge into confusion – although she probably wasn’t expecting her top lieutenant to be responsible.
“John Swinney might claim he misheard, but it’s clear that the SNP is making it up as it goes along in a desperate attempt to placate ultra-nationalists.”
Elsewhere, James Mitchell, professor of public policy at Edinburgh University, criticised the SNP’s “de-facto referendum” plans.
He told ITV Border: “There is no such thing as a de-facto referendum. There are elections and there are referendums and they are quite distinct.”
Prof Mitchell added: "It's not for a political party to dictate the terms of an election.”
Ms Sturgeon had earlier contrasted her desire for a “lawful” second vote on Scottish independence with the Prime Minister “breaking the law” by reneging on the Northern Ireland Protocol.
Her comments came as she agreed with Boris Johnson when he said Russian president Vladimir Putin would not have started the “crazy, macho” war in Ukraine if he were a woman.
Ms Sturgeon said: “Not that women don’t make mistakes, but I do think women tend to bring perhaps a bit more common sense and emotional intelligence and more of a reasoned approach to decisions.
“Take the difference between me and Boris Johnson on the big matters of the constitution. He is breaking the law to renege on the Northern Ireland Protocol, I am being very clear that any vote on independence has to be lawful.
“More women in leadership would be a good thing, including in the UK, so maybe it is another reason why he should do the right thing and step aside.”