Correspondence released by the Government has highlighted tensions between the HSE and NPHET over governance.
Letters from HSE CEO Paul Reid to Jim Breslin, the Secretary General of the Department of Health, dated April 19, states Mr Reid was "extremely disappointed" in the Chief Medical Officer, Dr Tony Holohan.
Mr Reid's major concern was around the National Public Health Emergency Team's (NPHET) public commitment to increase to 100,000 the number of Covid-19 tests per week, which he says was not what was agreed at Cabinet Sub-Committee level and in meetings with the Secretary General to the Government, Martin Fraser.
He added he was "regrettably, taken very much by surprise" by Dr Holohan’s letter, where he laid out the commitment, which he received after the NPHET press conference where the increase was discussed publicly.
"The directions as set out in the above letter and press conference are at odds with the process that we have been jointly engaged in. They are also at odds with the process in place with the HSE Board," Mr Reid wrote.
Given that all of this was agreed, I am extremely disappointed that these understandings appear not to have been respected.
"I’m at a loss as to why this direction from the NPHET to the HSE was given and publicly communicated without completing the jointly agreed processes and without regard to appropriate governance."
Mr Reid said the directions set out effectively attempted to commit the HSE to an intensity of implementation "which bears absolutely no resemblance to that which we previously discussed and has taken no account of what can be achieved by when".
Mr Reid said the development pointed to "the need for far greater cooperation" between the agencies.
He also called for a meeting with Mr Breslin to discuss the matters raised in his letter as a matter of urgency.
Likewise, a letter from Ciarán Devane, HSE Chairman to Health Minister Simon Harris, dated April 20, called on the Government to intervene in the strained relationship between the two.
"I write to suggest improvements to the nature of the relationship between NPHET and its stakeholders, including the HSE," the letter reads.
"It has been clear to me and to the Board of the HSE for a while that operational requirements have at times not adequately been considered at the centre of NPHET’s decision-making.
In this current situation a determination was announced in public which went even further than the letter which the HSE was surprised to receive after the event.
"Both cut across and pre-empted the process which had been agreed to develop the implementation plan in order to meet and exceed the target of 100,000 tests per week."
The letters were published following several requests from the Labour Leader Alan Kelly, who described their contents as "explosive" in the Dáil and say raises serious concerns about governance.
When asked about the letter on Newstalk radioshow The Hard Shoulder, Mr Reid played down the issue, and said although there had been tensions, that is to be expected.
"I would be a fool to think there wouldn't be tensions between a major agency and a department and there will be more," Mr Reid said.
"The reality is, what we were working through them, of course, there were tensions, but this was about making sure we had capacity.
"The outcome has been, over the last number of weeks, to have a shared plan which we published today.
"Absolutely there have been tensions in between, many tensions in various stages as big agencies working with departments but the outcome has been what we wanted to achieve."