Mr Johnson, speaking during Prime Minister’s Questions, made a dig at the SNP, claiming school pupils’ performance in maths and science are at a “record low” in Scotland under their governance.
The PM asked why SNP Westminster leader Ian Blackford was “so obsessed with breaking up our union rather than delivering for the children and pupils of Scotland”.
As Mr Blackford was called to speak, one of his colleagues next to him repeated “desperate liar” three times in remarks caught by Commons microphones.
Official parliamentary rules say that calling another member a liar is “unparliamentary language”, meaning the speaker would normally call on the MP using the language to withdraw what they have said.
The MP in question was not called up - possibly because speaker Sir Lindsay Hoyle didn’t hear the remarks.
Mr Blackford then accused Mr Johnson of having “no respect” for the people of Scotland and complained of the PM’s decision last week not to grant powers for Scotland to hold a second independence referendum.
The SNP and the Tories have a recent history of bad-tempered clashes in the chamber.
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Earlier this month, Tory MPs drowned out Brendan O’Hara with cheers after he name-checked Margaret Thatcher while trying to argue for independence.
Last month, Mr Blackford also called out Mr Johnson for “playing” on his phone rather than listening to his calls for independence. Mr Johnson, after putting his phone away, could be heard jibing back: “Say something more interesting.”