Leo Varadkar has claimed he "didn't say a bad word" about Chief Medical Officer Dr Tony Holohan as the Tánaiste was grilled on the public disagreement between the Government and the National Public Health Emergency Team (Nphet).
Opposition TDs laughed and jeered at Mr Varadkar as he made the remark during Leaders' Questions in the Dáil.
He said Sinn Féin was trying to engage in a blame game and failed to answer a question from Social Democrats co-leader Catherine Murphy as to whether he now regretted his remarks in a TV interview with RTÉ's Claire Byrne on Monday night.
Mr Varadkar slammed the Nphet proposal that the whole country move to Level 5 Covid-19 restrictions during the interview, as well as the manner in which that advice leaked to the public on Sunday night.
His remarks have been interpreted as severe criticism of Mr Holohan.
Mr Varadkar told the Dáil that Mr Holohan is "someone I respect immensely", saying he had worked closely with him in the past on controversies relating to Portlaoise Hospital and CervicalCheck.
He told Sinn Féin this was "when you were taking lumps out of him".
Mr Varadkar said the two men had had a good personal conversation in a telephone call on Tuesday night.
"Neither of us has any issue with the other, and we spent most of our telephone conversation talking about how we're going to beat this virus," he said.
Mr Varadkar admitted he had been told about the emergency Nphet meeting the day before it happened, but had no idea that it would recommend going to Level 5.
He said the leaking of that advice had "caused fear and anxiety and panic" for members of the public who thought they would be out of work the next day.
That was a shock and it had come out of the blue, Mr Varadkar insisted.
However, he added: "The events of Sunday and Monday are a distraction from what we need to do, and that is to fight the coronavirus together. Everyone against a common enemy, and that is what I want to do."
He said Sinn Féin "may want to make a big deal about which minister knew what and at what time on Sunday, but that's not the point".
"The point is we had no indication, until Sunday, that this was even being considered," he said.
"But we need to move on. This shouldn't be Nphet versus the Government, it shouldn't be the Government versus the Opposition. This has to be Ireland versus the coronavirus."