The Minister for Health is to make a statement to the Dail later to clarify his communications with the chief medical officer.
It comes amid growing confusion over what the Government was told by the National Public Health Emergency Team (Nphet) last weekend.
It emerged that the chief medical officer (CMO) Dr Tony Holohan spoke to Stephen Donnelly by phone three times on Saturday and Sunday, during which he raised concerns about the number of Covid-19 cases in Ireland.
But the Tanaiste and some Government ministers claim they were not made aware of the advice until Sunday evening.
Tanaiste Leo Varadkar said the recommendation from Nphet to move to Level 5 "hadn't been thought through and there hadn't been prior consultation".
Mr Varadkar said that nobody in Government had any indication that a Level 5 move was being considered until Sunday night.
"It came three days after Nphet recommended that it did not strongly support a move to Level 3 nationally at that time," he added.
"To make it clear, I was informed on Saturday, as was the Taoiseach and the Green Party, that a meeting of Nphet was called for Sunday. There was no suggestion, not even an inkling, that Level 5 was being contemplated.
"Had we known that, we would have sought an urgent briefing that night."
Sinn Fein's Pearse Doherty said Mr Varadkar's claim that Nphet's advice came out of the blue was "not the case".
"We know the CMO informed the Minister for Health on Saturday and we know he was spoken to before and after the Nphet meeting," he said.
"Everything that he (CMO) could have done he did in keeping the Government in the loop.
"When Nphet's recommendations made its way to Government, it was only then that it was leaked and for 24 hours after the Government said nothing."
Mr Doherty also accused Mr Donnelly of allowing the "perception to prevail" that the advice came out of the blue.
Mr Varadkar also said he "didn't say a bad word" about the CMO.
"We spoke on Tuesday night and we cleared the air. Neither of us has any issue with the other," Mr Varadkar added.
Social Democrats co-leader Catherine Murphy asked Mr Varadkar if he regretted making his comments about Dr Holohan.
She said Mr Varadkar's comments had been a "distraction" to tackling Covid-19.
Dr Holohan said on Wednesday that he had shared his concerns and those of other Nphet members with Mr Donnelly.
Dr Holohan also said that the Health Minister did not set out parameters in which they could conduct their meeting.
"I wouldn't pre-empt a conversation but I was very clear about the level of concern that I had and have, and if anything the level of concern I had then is less than the level of concern I have now," Dr Holohan added.
Green Party leader Eamon Ryan also said today that the Government was not made aware of Nphet's advice to move to Level 5 until Sunday evening.
"We had our meeting and Government took a different view. We are not ignoring the advice, but we are looking at other issues," he added.
"We decided to move to Level 3 and we hope that the numbers will stabilise."
He said that Government was "all on the same team", despite what the Tanaiste had said on Monday.
Members of Nphet are meeting on Thursday to discuss the track of Covid-19 across the country.
The latest figures from the Health Protection Surveillance Centre (HPSC) show that the national average rate of Covid-19 cases is 124.4 cases per 100,000 population.