NPHET had warned the Government that introducing level five restrictions now was the "only opportunity" to get the disease under control while keeping schools and other healthcare services open.
Health officials said a 'graduated approach' will ultimately lead to level five restrictions anyway.
The Chief Medical Officer's letter to the Health Minister was published as the Government confirmed they had rejected the level five recommendation.
Instead, they've decided to move the entire country to level three restrictions, with increased enforcement of the rules.
Advising stricter restrictions, Dr Tony Holohan told Stephen Donnelly that the rate of cases among people over the age of 65 has increased by more than 1,000 percent in the past two months.
He noted recent outbreaks in the likes of nursing homes, direct provision centres, homeless accommodation and among the Traveller community.
He also pointed to the increasing number of hospital admissions, and an increase in the number of COVID-19 deaths being reported.
Extract from Dr Tony Holohan's letter to Stephen DonnellyAccording to the letter, modelling has shown the country could be facing 1,600-2,300 new cases per day if current trends continue - as well as 43 people being admitted to hospital with the virus.
Dr Holohan said: "The NPHET believes that proactive and robust measures now be taken such that a very significant suppression of the disease with a reproduction number well below 1.0 is achieved."
He said that NPHET is 'sensitive' to the impact of another effective lockdown.
However, he argued that a move to level five for four weeks is "the only opportunity to get this disease back under control while keeping schools open, keeping health services for non-COVID activity operation and protecting the medically and socially vulnerable."
He noted that a graduated approach would ultimately "result in application of level five measures as mitigation", as it would not have a sufficient or timely impact.
You can read the full letter here.
'This hasn't damaged the relationship'
Tánaiste Leo Varadkar last night told RTÉ that the proposals from NPHET were "not thought through".
However, Health Minister Stephen Donnelly played down any rift between NPHET and the Government.
He said: "This hasn't damaged the relationship.
"We live in unprecedented times, and the types of decisions Government are being asked to make... are unprecedented decisions.
"I would expect robust debate and interrogation."
In his address to the nation, Taoiseach Micheál Martin acknowledged NPHET's recommendation - saying there was no doubt there was a need to alter the concerning coronavirus trends in most parts of the country.
However, he said the response has to be "effective and proportionate".
In terms of a potential move to level five, Mr Martin said: "It could involve the loss of hundreds of thousands of jobs, with these concentrated in families and communities which are already facing difficulties.
"An immediate comprehensive lockdown would make it much harder to deal with non-COVID health concerns including the impact of isolation on the mental health of many of our people."
Level three restrictions will come into effect from midnight tonight for three weeks.
