Labour MSP Neil Findlay used the language - deemed un-Parliamentary by Presiding Officer Ken Macintosh - as Ms Freeman faced questions at Holyrood on the use of vaginal mesh implants.
Mr Findlay hit out amid claims that Chief Medical Officer Catherine Calderwood had suggested that a ban on use of mesh was only temporary. This appeared to contradict assertions Ms Freeman had previously made at Holyrood that the procedure would not be re-introduced.
"Which one is it?"
The outburst came under fire from Presiding Officer Ken Macintosh who insisted that the term lying is "not acceptable" in the Holyrood chamber.
He then allowed the question session to resume for just over ten minutes before returning to Mr Findlay.
"I've given you a few minutes to calm down, to reflect," the Presiding Officer said.
"I would ask you to withdraw the remarks you made and the accusations you made earlier."
"Presiding Officer you know I have great respect for you and the office you hold and I have great respect for the women who have been injured by mesh," Mr Findlay said.
"They have made a similar statement in the media about two weeks ago to the one I made. The cabinet Secretary has to be held to account for her actions.
"An apology to yourself Presiding Officer, but I'm very sorry I cannot withdraw the comment."
Mr Macintosh then ordered the MSP out.
"I'm sorry Mr Findlay that's not acceptable I'm afraid I'll have to ask you to leave the chamber."