The HSE first became aware as far back as November that thousands of women will now need repeat smear checks, the Tánaiste has confirmed.
Around 6,000 women will be written to next week after it was revealed that their slides were not checked within the acceptable timeline when they were sent to a US lab.
The women impacted by the latest CervicalCheck controversy had all been asked to get a secondary HPV test after low-grade changes were detected in their initial smears.
The test for HPV should be carried out within 30 days of the sample being given by a woman but it has now emerged Quest Diagnostics failed to meet this deadline in the case of 6,000 samples which were taken from 2015 onwards.
Simon Coveney told the Dáil that concerns were first raised in November but said it was "not true" to give the impression that "somehow the Government is trying to hide something and we would not be talking about this if it had not been for the Fianna Fáil leader raising it".
"The HSE stated it was made aware of this matter in November and the Minister was made aware of the issue with secondary HPV testing in December," Mr Coveney said. "The issue was discussed at the CervicalCheck steering committee, including with patient representatives who are working very hard on that committee on the range of issues involved and outlined in published weekly reports.
"The Minister sought regular updates but a final report was not available to him relating to the numbers involved or who they were."
He said the latest controversy is separate to the current delays of up to 22 weeks for smear test results which has been caused by a surge in the number of women seeking tests in the wake of the initial CervicalCheck scandal.
"My understanding is that the challenge has been at the lab level, and this is not about resources; rather it relates to the capacity of labs."
He said GPs have coped "extremely well" with the extra demand from an increase in women coming forward since the summer.
Fianna Fáil deputy leader Dara Calleary accused the Government of creating a gap between promises and delivery which "thousands of women are falling into".
"The Government has failed to draw a clear line under the controversy. It made significant promises but did not put the resources necessary in place to back them up. Now, we are in a situation of concern."
Sinn Féin's Pearse Doherty said the latest controversy is "another example of the incompetence that prevails in a chaotic system".
"Mistakes have occurred and will continue to happen in the health service but we have just emerged from a major scandal and many women are still dealing with its consequences. People have lost their lives because of the CervicalCheck scandal and now we have found out there are another 6,000 women who must have a secondary test done again because the lab got things wrong," Mr Doherty said.
Pointing to the fact that this is Cervical Cancer Prevention Week, Labour leader Brendan Howlin said the ongoing delays in cervical cancer screening have forced some women to get privately tested. He said this is not an option to everyone adding that this is "another example of a two-tier system".
He asked Mr Coveney if the Government will now refund women who decide to get private smear checks. The Tánaiste did not respond to that.