That is despite Tánaiste Leo Varadkar saying the proposals from chief medical officer Dr Tony Holohan were "not thought through".
Every county in Ireland will enter Level Three restrictions from midnight tonight.
I would expect robust debate and interrogation
However, they rejected the Level Five measures proposed by NPHET. The group had recommended that the country be placed under the stricter Covid-19 restrictions for a period of four weeks.
Health Minister Stephen Donnelly played down any rift between the public health officials and politicians.
"No, this hasn't damaged the relationship [between NPHET and the Government]," said Mr Donnelly. "We live in unprecedented times and the types of decisions Government is being asked to consider and the types of decisions that are being made, and that we are all talking about now, are unprecedented decisions."
He added: "I would expect robust debate and interrogation."
During an appearance on RTÉ's Claire Byrne Live last night, Tánaiste Leo Varadkar was critical of Dr Holohan's proposal for a national implementation of Level Five restrictions.
He said: “It was landed on us on a Sunday night as a surprise and without consultation.”
Mr Varadkar described the Level Five lockdown plan as a “circuit breaker strategy” and “experimental”, he added that such a move “requires proper thought, prior consultation and a Plan B if it doesn’t work and we’ve not had any of that”.
He denied that the Government was gambling with people’s health. “I think what we’re doing is very much in line with what’s recommended by the World Health Organisation and the ECBC." But in terms of economics, he said: "We can’t say for certainty if the country can afford a second lockdown."
Denying that the decision is being made between economy and public health, Mr Varadkar said it was about “public interest always first”.
“My view on this from day has been the same: put public health first. Our economy will not do well if people are sick, customers are sick and staff are sick. But it can’t be public health only. We have to bear in mind the long-term impact of a prolonged second lockdown.”
When Claire Byrne asked him directly about the relationship between Government and NPHET, Mr Varadkar replied: “We are all good people, we all want what’s best, and we all want to avoid long-term damage that will cost lives”. He said that after today's meeting “the CMO accepts that and you won’t see a repeat of this sort of thing."
None of those people, for example, would have faced being on the Pandemic Unemployment Payment benefit
When Mr Varadkar was asked whether he had confidence in NPHET, he replied: “I have confidence in NPHET to dispense public health advice, but that is what they do. They don’t advise the public, they advise the Government and the Government decides. One thing that needs to be borne in mind is that these are very good people – 40 of them – but all coming from medical, scientific or civil service backgrounds.
"None of those people, for example, would have faced being on the Pandemic Unemployment Payment benefit, none of them would have to tell somebody that they are losing their job, and none of them would have to shutter a business for the last time. And I’m not talking about the economy, I’m talking about something that could have happened to half a million human beings from tomorrow.
"Sometimes the reason why politicians make these decisions is because we are the ones who can see the bigger picture. It’s not just about a virus and statistics around the virus, or death rates, it’s about real people and how it impacts on so many different people and so many different communities in so many different ways.”
"The potential implications of such a move are severe and very different from those we faced earlier this year," Taoiseach Micheál Martin said in an address to the nation last night.
"The road ahead will continue to have many turns," he said. "If we all act now, we can stop the need to go forward in introducing further Level Four and Level Five restrictions."
