In a letter to Health Minister Stephen Donnelly he estimated that up to 500,000 people got the virus last week as the Omicron variant swept the country.
It comes a day after Ireland passed one million Covid cases since the start of the pandemic, with more than 1,000 patients in hospital for the first time, and as the World Health Organization said more than half the population of Europe would get Omicron in the next six to eight weeks.
Dr Holohan also said that while all face masks can significantly reduce transmission of the virus, as long as they are well fitted and worn properly, medical grade or respirator masks, such as the FFP2 version, are more protective.
He suggested that people over 60 or those who have an underlying condition may prefer a respirator mask.
These are disposable and are more expensive than regular masks.
The National Public Health Emergency Team (Nphet) is to do an analysis of what is known about the Omicron variant as well as the impact of vaccines, including boosters, when it meets later this month.
He told the minister that deaths and intensive care admissions are stable and Omicron has a lower intrinsic virulence.
However, he expressed concern about the number of patients who are picking up the virus in hospital, pointing to 36 of these infections in the week before Christmas.
Meanwhile, new guidance says that staff in nursing homes should wear respirator face masks.
The guidelines which come in on January 17 say staff can wear surgical face masks when they are with other staff but have the FFP2 or similar masks when in patient care.
The guidance from the Health Protection Surveillance Centre (HPSC) also said residents who get the virus but are fully vaccinated with a booster shot can reduce their period of self-isolation from fourteen to ten days.
This is also the case for fully vaccinated residents who have had Covid-19 and must wait before they get a booster shot.
Dr Holohan’s letter said that people had a quieter Christmas and a range of mobility data suggests that socialising across a number of settings fell over the festive period and New Year.
As of January 5 last there have been a total of 5,952 Covid-related deaths notified in Ireland.
This is an increase of 40 notified deaths since the previous weekly update on December 29.
Dr Holohan said 157 deaths had been notified which occurred in December 2021.
He also referred to the online system for people taking antigen tests to report their results.
An average 8,408 are reporting their results daily and 80.5pc of those whose antigen test showed a positive result had it confirmed after getting a PCR test.
Around 229,113 people were named as close contacts of a confirmed case between December 27 to January 2, an increase of 123pc over the previous week.
Currently PCR testing capacity is at 300,000 a week and use of antigen tests has increased to 350,000 a week.
Test positivity is increasing among all age groups, with rates greater than 50pc in those aged five to 54.
It has also increased in the over 65s in recent weeks.