Chief Medical Officer Dr Tony Holohan said NPHET's findings and recommendations on Sunday required "early, serious and confidential discussion".
"That didn't happen," he said.
"The content leaked into the media and whoever was responsible for that leak does not share our objective to deal with the disease."
Dr Holohan said NPHET would continue to make its conclusions and findings available to the Minister for Health in the "usual way".
"We look forward to getting back to work."
Tánaiste Leo Varadkar has said he was "really unhappy" about what happened on Sunday night when NPHET recommended the entire country should move to Level 5 virus restrictions, but he had spoken to Chief Medical Officer Tony Holohan last night and both men "are on the same team".
Mr Varadkar was responding to a question at the launch of the Climate Action Bill this afternoon.
He was asked about his comments earlier this week when he said the recommendation from the National Public Health Emergency Team to move to Level 5 "hadn't been thought through and there hadn't been prior consultation".
In an interview on RTÉ's Claire Byrne Live, Mr Varadkar said what happened was not good for the Government, NPHET or the Irish people and he said it "came out of the blue".
Asked about comments he made this week about NPHET, Tánaiste Leo Varadkar says he was 'really unhappy' about what happened on Sunday night, but he spoke with Chief Medical Officer Dr Tony Holohan last night and both men are ‘on the same team’ | Read more: https://t.co/6efMFrL4ZG pic.twitter.com/mWfsXHLCGu— RTÉ News (@rtenews) October 7, 2020
Earlier, Taoiseach Micheál Martin also paid tribute to Dr Holohan, saying he met him this morning and they had a "good meeting".
Mr Martin said they "share a determination" to tackle Covid-19.
Taoiseach Micheál Martin says he met Chief Medical Officer Tony Holohan this morning and they had a "good discussion", adding "I pay tribute to his commitment to the country" | https://t.co/F817ZTGkOp pic.twitter.com/LcQBpQlJ44— RTÉ News (@rtenews) October 7, 2020
There had been criticism of Mr Varadkar's comments about NPHET and Dr Holohan on Monday.
Mr Varadkar's remarks followed NPHET's recommendation on Sunday to put the country under Level 5 restrictions, however the Government decided to move to Level 3 instead.
During today's briefing, Dr Holohan's first since returning from a period of leave, the Chief Medical Officer said he was "deeply indebted" to the Deputy Chief Medical Officer, Dr Ronan Glynn and to his family "for the work that he has done and that his family has supported him in doing".
"This enabled me to be in a position to spend time with my family and it will not be forgotten."