Serious and confidential discussion did not happen because whoever disclosed the guidance did not share their objective of tackling Covid-19 the Chief Medical Officer added.
He said he enjoyed a good relationship with Tánaiste Leo Varadkar.
Dr Holohan said: “We conveyed our findings, analysis and recommendations to the minister for health and on to Government.
“They required early and serious confidential discussion.
“That didn’t happen because the information leaked into the media on Sunday evening.”
Mr Varadkar has said the recommendation from the National Public Health Emergency Team (Nphet) to move to Level 5 “hadn’t been thought through and there hadn’t been prior consultation”.
He added on Wednesday: “I was really unhappy, really unhappy about what happened on Sunday night and the anxiety and fear that it caused for hundreds of thousands of people and I gave voice to that anger and gave voice to that frustration.
“But I also said that Nphet and the Government needed to get back on the same page. I rang Tony Holohan last night. We had a good conversation.
“We’re on the same team. We always have been and what we need is not the Government versus Nphet, it’s Ireland versus Covid.”
Dr Holohan said he had a long-standing and good relationship with the Fine Gael leader.
He added: “He understands and shares my analysis every bit as much and has as much concern as I do about it.
“We have a job, which is to make an assessment of the disease.
“Government has to consider a range of other considerations to come to a balanced decision.”
He added that he also had a thick skin and his team of experts was committed to making the Government’s latest decision a success.
Another five deaths and 611 cases of Covid-19 have been detected.
Dr Holohan said: “All key indicators of the disease have deteriorated further in the three days since the last meeting of Nphet on Sunday October 4th.
“Covid-19 is spreading in our community in a very worrying manner. We have to break these chains of transmission.”
Case numbers and admissions to hospital are growing “exponentially”.
Professor Philip Nolan, who is modelling the disease’s spread for the Government, said: “The reproductive number is now estimated at 1.2.
“Case numbers and hospitalisations are growing exponentially. The Reproductive number is now estimated at 1.2. If we fail to reduce viral transmission nationwide immediately, we could see 1,100 – 1,500 cases per day and 300-450 people in hospital by November 7th.”@President_MU
— Department of Health (@roinnslainte) October 7, 2020
“If we fail to reduce viral transmission nationwide immediately, we could see 1,100-1,500 cases per day and 300-450 people in hospital by November 7th.”
The number of people in hospital has increased from 122 last Thursday to 156 on Wednesday afternoon.
There are 25 people in critical care compared with 20 one week ago.
Dr Holohan said 80 Covid-19 cases were admitted to hospital in August, 206 in September and 77 so far in October.
“In August, four Covid-19 related deaths in total were reported, 34 in September and today on October 7th we report eight Covid-19 related deaths this month.”
He said he loved the job he was doing and would not forget his treatment by the Government in allowing him to take time off to care for his sick wife in the midst of the pandemic.