Nicola Sturgeon indicated EU nationals were "bargaining chips" during the Scottish independence referendum, the Home Office has claimed.
Immigration minister Robert Goodwill attempted to counter SNP condemnation of the UK Government's approach to post-Brexit rights for EU nationals living in the UK by citing comments from the First Minister.
He suggested in 2014 that Sturgeon, then deputy first minister, cast doubt on the future of 160,000 EU citizens living in Scotland.
She said: "We have set down a robust and common sense position.
"There are 160,000 EU nationals from other states living in Scotland, including some in the Commonwealth Games city of Glasgow.
"If Scotland was outside Europe, they would lose the right to stay here."
Goodwill's accusation was rubbished by the SNP's justice and home affairs spokeswoman Joanna Cherry, who insisted her party's long-standing policy has been to ensure equal rights for all living in Scotland.
The row surfaced as the SNP led a Commons debate calling on ministers to ensure all EU nationals living in the UK retain their existing rights after Brexit.
Around three million EU citizens are waiting to find out if they can remain in the UK, with the overnment seeking to guarantee the futures of Britons living overseas as part of Brexit negotiations.
This has led to claims that ministers are using EU nationals as "bargaining chips".
Cherry told the opposition day debate: "I use the words 'bargaining chips' advisedly because it's a source of shame to this House and the United Kingdom that the Prime Minister and several of her ministers, including the right honourable member for Haltem Price and Howden (David Davis) and, I'm particularly ashamed to say the honourable member for Dumfriesshire, Clydesdale and Tweeddale (David Mundell) have hinted at using EU nationals living in this country as bargaining chips.
"Indeed, at the Conservative party conference... the honourable member for North Somerset (international trade secretary Liam Fox) went so far as to compare the European Union nationals to cards in a game."
Goodwill, intervening, said: "You talk about European citizens being used as bargaining chips.
"Do you recall that in 2014, Nicola Sturgeon herself threatened to strip EU nationals of their right to remain in an independent Scotland?"
SNP MPs shouted against Mr Goodwill's remark, with the Tory frontbencher adding: "As reported in the Scotsman newspaper, she said: 'There are 160,000 EU nationals from other states living in Scotland including some in the Commonwealth Games city of Glasgow. If Scotland was outside Europe they would lose their right to stay here'.
"Who is being used as bargaining chips?"
Cherry replied: "Can I in the gentlest and friendliest way, counsel you against taking advice firstly from the Conservative party in Scotland, and secondly from the Scotsman newspaper which is, frankly, not what it was when I was a girl.
"There is absolutely no question that the First Minister Nicola Sturgeon or her predecessor (Alex Salmond) ever threatened EU nationals with not being part of Scottish society.
"Our policy has been clear for many, many years - that we want an independent Scotland inside the European Union with equal rights for all living in Scotland.
"We're quite clear on that. What this debate is about today is making the UK Government clear on having equal rights for all across the United Kingdom."