The Taoiseach has said the move by Dr Tony Holohan to Trinity College in Dublin should be paused while a report on the appointment is carried out.
Micheál Martin said the planned academic role for the Chief Medical Officer should be reassessed and that there needed to be greater transparency around the appointment.
Earlier this week, the Minister for Health Stephen Donnelly defended the decision to allow Dr Holohan to move to Trinity College while the Department of Health continued to pay him his Chief Medical Officer salary.
This morning, the Taoiseach revealed he has asked Mr Donnelly and the Secretary General of the Department Robert Watt to carry out a report into the appointment by Monday.
Speaking in Helsinki, Mr Martin said the research element of the role must be teased out and that he believed it was more than just a personnel issue.
The Taoiseach said he had not commented until now on the matter, because he had not received all the details "behind it".
Afterwards, Tánaiste Leo Varadkar said pausing the appointment was the right decision and that the Government needs to reassure itself that the correct procedures were followed.
"Because it does involve taxpayers' money, we think it's appropriate that the appointment should be paused for a short period, so we can find out exactly how it came about and to reassure ourselves that the correct procedures were followed," Mr Varadkar said.
"I'm sure they were, but we want to be sure of that."
Mr Varadkar said that both he and Mr Donnelly had made the "reasonable assumption" that a post had arisen in Trinity College and Dr Holohan has applied for it and got the role, but he said it "appears to be a bit more complicated than that".
"Nobody in Government is happy about this, because even though we are not involved in it in any way, inevitably these things do reflect on us because we are the politicians in charge and that's why the Taoiseach took the decision to pause the appointment until we get a proper understanding on what happened here and whether procedures were properly followed," Mr Varadkar added.
He added that it was "very much the role" of the Secretary General to look after personnel matters and there is a clear division of responsibility in Government departments
The Sinn Féin Leader has said the Government must change its culture when it comes to appointments and take responsibility for how they are made.
Mary Lou McDonald said there was a "pattern of behaviour" where members of Government have been involved in appointments and pay hikes which, she said, were "outside of the established procedures".
"Hand-wringing after the event isn't going to convince anyone and Government need to learn and act in accordance with the fact that public appointments when using public money have to be transparent and it has to be done by the rule book for everybody," Ms McDonald said.
She added that "looking for a fall guy" was a failure of the Government to take responsibility.
Ms McDonald said she thought that Dr Holohan was an accomplished public servant and that the idea of the post was a wise one, but she said this was about proper procedure and respecting that there are rules and that the Government have to play by those rules.
"This has to be a moment finally where there is a sea change in how Government does business," she said.
"We have had, time and time again, ministers and the party leaders involved in pay increases, pay hikes and appointments that didn't tally with the rule book. That can't happen."
Ms McDonald added that if it was a permanent post, that she believes that Trinity College should pay for the post.
Labour's Health Spokesperson, Duncan Smith, said there needs to be transparency around the appointment of Dr Holohan to the academic role because of what he described as the Government's poor record on appointments in the Department of Health and beyond.
He said it was the right decision to pause the move until a full report was carried out and made public.
Mr Smith said while the role could be a good thing for the State and Dr Tony Holohan is uniquely placed to be a a part of, it he said there needed to be more information on what benefit the public will get from the role if the Department of Health is paying for it.
In a statement, the Department of Health said the report will be submitted to the minister in due course.
In response to the recent developments, Trinity College Dublin said all questions about the secondment should be addressed to the Department of Health.