Taoiseach Micheál Martin has said it is regrettable that Chief Medical Officer Dr Tony Holohan will not be taking up his role with Trinity College Dublin, but he said there should have been transparency on the details from the outset.

Dr Holohan announced yesterday that he would retire as CMO in July instead of taking up the secondment to Trinity as Professor of Public Health Leadership and Strategy.

On Friday, Mr Martin said the appointment should be paused pending the completion of a report by the Department of Health.

Speaking in Dublin this afternoon, the Taoiseach said if there was a broader deliberation on the position, it could have turned out differently, adding that lessons would have to be learned.

Mr Martin said his understanding was that the salary was to have come from Exchequer funding into the Department of Health and it would be paid multi-annually through the Health Research Board.

Asked about Department of Health Secretary General Robert Watt, the Taoiseach said he did have confidence in him and he was a very capable public servant.

Mr Martin said he had not spoken to either Dr Holohan or Mr Watt.

He said there was a lot of surprise at the manner in how the details of the arrangement emerged.

Sinn Féin's health spokesperson David Cullinane said Dr Holohan's decision to retire was a loss to the public system, but that the circumstances that led to his resignation were "entirely the making of very senior civil servants".

Mr Cullinane said the Minister for Health has serious questions to answer, adding that he believes senior civil servants are "running rings" around Stephen Donnelly.

Speaking on RTÉ's This week programme, Mr Cullinane said: "We have, in my view, not the minister in charge. We have senior officials in the HSE and the department running the show, and that's not the way it should be."

Mr Cullinane said that there had to be fair procedures around public appointments and issues in relation to the public pay of senior officials.

Meanwhile, a Fianna Fáil TD and member of the Oireachtas Health Committee said Dr Holohan's experience would have been invaluable to the proposed new role.

However, John Lahart acknowledged that the perception of the process by which Dr Holohan was appointed to the job was flawed and said the Government's handling of the issue was "ham-fisted".

Speaking on the same programme, former director general of the HSE Tony O'Brien said public health policy could have really benefitted from Dr Holohan's contribution to Trinity.

Mr O'Brien said: "The amount of knowledge and learning that Tony Holohan has gained in the last couple of years, as well as throughout his career as Chief Medical Officer, leave him uniquely well placed to play a role in forward preparedness for future pandemics but also in providing a focus for academic leadership in the discipline of public health."

He said he was disappointed but not surprised at Dr Holohan's decision not to go ahead with the position and that the Taoiseach's comments on Friday left him with no other option.

Mr O’Brien told This Week that Dr Holohan's particular skill set and experience means he is effectively irreplaceable in the process, adding that he is one of a very small number of people in the department who is a civil servant but also a trained medic.