The comment came as Eleanor Laing, who was standing in for speaker Lindsay Hoyle while he recovers from Covid, gave Flynn the floor to ask a question of Rishi Sunak.
She introduced the “leader of the Scottish nationalists, Stephen Flynn”.
In the past, Hoyle has told off Tory MPs for referring to the Scottish National Party in an improper way. Disgraced former prime minister Boris Johnson was frequently admonished for describing the party as the “Scottish nationalist party”.
There are also multiple MPs in the Commons who believe in Scottish independence and who are not led by Flynn. These include Alba's two MPs, Neale Hanvey and Kenny MacAskill, and the now-independent Western Isles MP Angus MacNeil.
An Alba spokesperson quipped that SNP MPs “no longer view themselves as nationalists”.
They said: “I am sure this is but a mere slip by the normally ever so eloquent Eleanor Laing.
“The current SNP have made it clear that they no longer view themselves as nationalists, and despite a few honourable exceptions on the SNP benches, our two Alba Party MPs and Angus Brendan MacNeil are the only Scottish nationalists in the House of Commons. “
A spokesperson for the Westminster speakers’ office told The National that Laing had “made a slip of the tongue for which she has apologised to the SNP”.
They added that the SNP had accepted the apology.
After the slip, Flynn pressed Rishi Sunak on migration policy.
The SNP group leader said it was “not just in relation to Margaret Thatcher where the Tory and Labour leader appear to agree”.
He went on: “The same is true of the government's latest migration policies.
“Now, for those of us on these benches, we aren't afraid to say that we believe migration is a good thing, it enriches our communities, it enriches our economy, it enriches our universities, our schools, our health service and of course, our care sector.
“So in that regard, can I ask the Prime Minister, why does he think it is acceptable to ask people to come to these shores to care for our family members whilst we show complete disregard for theirs? What has become of this place?”
The reference was to new Tory visa rules which mean people across the UK could see foreign partners told to leave the country the next time their visa comes up for renewal if their household does not earn at least £38,700.
Sunak insisted it is "absolutely right that we take strong action to curb the levels that we have seen because they are simply far too high and place unsustainable pressure on our public services".
He added: “I make no apology for saying that, or indeed saying that it is important that those who come here contribute to our public services.”