The HSE chief executive has apologised to 2,000 people for asking them to notify their own close contacts after testing positive for Covid-19 due to a breakdown in the contact-tracing system.
Paul Reid defended the way the HSE handled the matter, saying it had to make decisions "rapidly and quickly" to stay ahead of the virus.
He admitted the Government should have been informed and said he "took responsibility" for not doing so.
Mr Reid said: "I personally, and on behalf of the HSE, apologise to those 2,000 people.
"It wasn't a decision that was taken lightly but it was the right decision.
"It was a decision based on a clinical, an operational and a risk-based assessment of what was the right thing to do at that point of time as Monday moved into Tuesday and we were faced with a backlog with those number of cases."
He made the comments at a HSE briefing on Thursday afternoon.
It emerged earlier this week that the system had come under too much pressure at the weekend and about 2,000 who tested positive for coronavirus would not be contacted by the HSE's contact tracing team.
Instead they had to tell their close contacts to arrange their own test through their GP.
Mr Reid blamed a "scheduling issue" for the backlog and said the health service was also dealing with increased volumes of calls and that those calls had become more complex and longer in duration.
He said: "We did not have enough people to cope with the rapid acceleration of cases that we saw on Saturday, Sunday and Monday."
He added: "We are dealing and have been dealing with a pandemic that is practically out of control in the community and when it gets out of control it has significant impacts on the wider health service overall."
Taoiseach Micheal Martin and Minister for Health Stephen Donnelly only became aware of a breakdown in the contact-tracing system when it was reported in the media.
Mr Reid said: "Keeping the politicians, particularly the minister and the Taoiseach, advised of the quick pace we were dealing with this issue was something that didn't work as it should and I take responsibility for that."
Mr Martin said he was annoyed he had not been informed of the issue but that he understood the pressure the health service was under.
"Whilst I was annoyed with what happened, I was also annoyed with not having been told about it directly, at the same time I would like to acknowledge that people are working under great stress and strain at all levels since the pandemic began," he said.
Earlier Mr Donnelly said that his department should have been told by the HSE.
"There are numerous ways in which Government could have been told. I am in contact with multiple people in the HSE on an ongoing basis and so are people in the department," he told RTÉ's Morning Ireland programme on Thursday.
"This was an operational decision taken by the HSE on a Monday, but let's be clear, people are incorrectly saying the contact tracing system has fallen down, it absolutely hasn't.
"What happened was the contact-tracing teams are being ramped up very quickly.
"In the last six weeks they are now making 400% more calls than they did."
He said he had been assured by the HSE the incident will not happen again.