Dr Tony Holohan has revealed his biggest concern with antigen tests after NPHET's new advice to Government promoted the use of them.
The tests were labelled as "snake oil" earlier in the year by Professor Philip Nolan - but Dr Holohan, in his letter to the Minister for Health Stephen Donnelly on Monday evening, said that "the epidemiological situation in Ireland indicates a worsening disease profile with the future trajectory very uncertain".
As a result, the Government made the call to change how testing is done,
Previously, if a person was fully vaccinated and deemed a close contact of a confirmed case, there was no advice to get a test if there are no symptoms.
But in future, if people are deemed to be a close contact and are fully vaccinated, they will be sent a rapid antigen test.
Appearing on Today with Claire Byrne, Dr Holohan explained why the advice had changed - and gave a major reason for concern.
He said: "First off, if they're to be used properly by the public, it will hurt. You have to get a good sample.
"People are using antigen tests when they or their children are symptomatic - and then on assumption of a negative test, sending them into school.
"That is concerning because we are missing Covid, but we are also potentially missing flu. That is a very concerning practice. If you have symptoms, restrict your movements, get a PCR test, don't go for an antigen test."
Dr Holohan also confirmed that there have been cases of the new Covid mutation AY.4.2 found in Ireland.
AY.4.2 is a sub-variant of the Delta variant which caused carnage across Ireland in the early part of 2021.
Dubbed "Delta Plus" by some outlets, the variant is potentially a marginally more infectious strain, Professor Francois Balloux told the BBC.
