The Taoiseach said there should be "a reassessment" of the Tony Holohan appointment.
Micheál Martin has called on Health Minister Stephen Donnelly to furnish him with a report on Monday about how the situation came about.
Under pressure about the specifics of the agreement which will see Dr Holohan leave his post as Chief Medical Officer, the Department said discussions are underway with Trinity about who will pay Dr Holohan's €187,000 a year salary when he begins his job on July 1.
"I've asked the Minister for Health for a full report on the entire process that led up to this appointment and the minister has asked the Secretary General for that report," the Taoiseach said.
"There seems to have been a number of strands to this in respect of a research strand, and I think we all understand the merit in having creating additional capacity to and a greater research platform around pandemic preparedness, given the experiences that we've had over the last two years.
"Clearly, this was a very pivotal position in that regard.
"But there has to be transparency there has to be good process and procedure. I don't see this as just a human resource issue, or personnel issue in its own right, which I can understand.
"In my view, it should be paused it should be a reassessment as to how the objectives that are behind this can be realised in a better and more transparent."
The Taoiseach said there should be “an assessment of all of the aspects” of the appointment and that there was time to do this before Dr Holohan is due to take up the position at the start of July.
“I do believe there has to be full transparency in relation to it. and I think the research dimension of this needs more teasing out,” he said.
“I mean, I haven't commented so far until now because I wasn't fully apprised of the situation, didn't have the details behind it, and it seems to me, I'd like to see the full report on Monday, but it would make sense to me for it to be reassessed.”
The Chair of the Oireachtas Committee on Finance, Public Expenditure and Reform John McGuinness has said that the Department of Health Secretary-General, Robert Watt, and the Minister for Public Expenditure and Reform Michael McGrath will be asked before the committee to answer questions on the secondment of Dr Tony Holohan.
The decision to approve Dr Holohan's secondment to Trinity College Dublin was made by Mr Watt, it has been confirmed.
The Department said in a statement that the decision was made "at the highest level".
In an interview on Morning Ireland on RTÉ Radio 1, Mr McGuinness spoke of his “serious concerns” about how the secondment of Dr Holohan to Trinity College Dublin was handled by the Secretary-General of the Department.
“It is quite a mess within the Department. It shows a certain dysfunction within the department and we need to clarify it.
"I have serious concerns about how the Department reached the decision in relation to all of this and also the fact that the Minister (of Health) was not informed. Minister McGrath was not informed.
"There is still a lot of questions as to how this position was created and was funded. Why there was so much secrecy around it. Why the Department refused to answer questions from the very beginning.
"It shows a very poor performance in terms of management from the Secretary-General of the Department and there are questions that need to be put to him and need to be clarified.”
Dr Holohan announced last month that he is stepping down from his position as Chief Medical Officer (CMO) to take on the new role at Trinity College Dublin.
He will remain a civil servant and his €187,000 a year salary will be paid by the Department of Health. A private meeting of the Oireachtas Committee on Health yesterday heard that Mr Watt signed off on the controversial secondment of Mr Holohan to a role at Trinity College Dublin.
Mr McGuinness said that every Secretary-General has a responsibility to appear before Oireachtas committees.
“Mr Watt will be asked after the Easter recess but during the recess, we will be making arrangements for that to happen. And Minister McGrath will also be asked before the committee. And indeed if the Minister of Health had a role in this well we will need to know what that is too.
"But this cannot continue in terms of the management of any department. The Minister must be informed and there are certain guidelines and so on that need to be followed relative to appointments like this.“
Earlier this week Minister for Health Stephen Donnelly told RTÉ Radio that Dr Holohan’s new role as a Professor of Public Health Strategy and Leadership at Trinity College Dublin as a “really positive move” which he fully supports.
Yesterday Fine Gael senator Jerry Buttimer called for "accountability and transparency" in relation to Dr Tony Holohan's new role at Trinity College Dublin.
Senator Buttimer told the Claire Byrne Show on RTÉ Radio 1, that the handling of the situation by the Department of Health has been "absolutely appalling."
"Tony Holohan has given the State huge service and we thank him for that. It is not personal. But this is about accountability and transparency.
"From my understanding, there is a board of management in the Department (of Health) that are the executive of the running of the Department and I find it unbelievable that the Minister for Health wasn't told until Tuesday (that the Holohan post was a secondment).
"Why was that the case number one? Why didn't the Secretary-General tell his Minister? And thirdly why now at the beginning were we not told that this is a secondment?"
Senator Buttimer said that it was assumed that the position of CMO was being advertised because Tony Holohan was retiring.
"And then we discover it is a secondment. Then this morning we discover we are going to work in collaboration with the head of research with the universities which we all think is a great idea. But clarity is required on the process.
"Who authorised it? Was the job advertised? Why are Trinity College not paying the salary of a person who is now not going back to the job. It is not a secondment.
"We need to know why this wasn't communicated in the manner it should have been to the Taoiseach and the Minister."