The Tánaiste was accused of being "complicit or a stooge" in efforts to damage the Irish Medical Organisation (IMO) during a lengthy Dáil questions and answers session.
In a Dáil session focusing on Leo Varadkar's passing of a confidential document to the now-defunct National Association of GPs, Labour's Aodhán Ó Riordáin read a text message he claimed was sent by then NAGP president Maitiu O Tuathail, which allegedly said "I'd love to destroy the IMO".
The IMO was the Government's negotiating partner on the GP contract which Mr Varadkar gave to Dr Ó Tuathail last year.
Mr Ó Riordáin said that messages he had obtained pointed to Mr Varadkar being used by the NAGP.
"In a message to his colleague, Dr Ó Tuathail wrote "Leo constantly pulling strings for me. You’ve no idea". Is he over-egging the nature of his relationship with the Tánaiste? What are these strings which Dr Ó Tuathail suggests the Tánaiste pulls for him constantly?"
Mr Varadkar responded that Dr Ó Tuathail was "someone who is known to me, who is a friend but not a close friend".
Sinn Féin's Pearse Doherty asked why the Tánaiste sent the document to Dr Ó Tuathail's home address and not the NAGP office, which is across the road from the Dáil.
Mr Varadkar said that while his method wasn't the right way to send the document, he had done so "as a shortcut, in a way", saying that he was keen for NAGP doctors to get behind the deal.
Mr Doherty said that Mr Varadkar's defence that he had been engaging with the union was "ridiculous".
"This is old boys' club. This is not something that one just apologises for and try and make excuses that this was a part of an ongoing engagement. We now know there was no engagement."
Rise TD Paul Murphy asked Mr Varadkar if he was planning to sue, which published the original story. Mr Varadkar said that while he had "very strong legal advice that the front page is defamatory", suing the magazine would be "like suing someone on Twitter".