Opposition parties are now questioning if Minister for Health Stephen Donnelly is in control of the Department of Health following controversy surrounding a position in Trinity College offered to Dr Tony Holohan.
On Saturday, the chief medical officer (CMO) Dr Tony Holohan announced that he will not go ahead with a secondment to the academic role at Trinity College Dublin.
The Government had been dogged by questions in recent days over the move, including why the Department of Health was to fund the secondment.
Dr Holohan is also stepping down as CMO from July 1st, as he doesn't want to see the controversy of the last few days continuing.
Sinn Féin Health Spokesperson David Cullinane said that Dr Holohan's decision to not take the position was not unexpected.
"Obviously it is deeply disappointing for him and I think it is a loss to the public service that he will now be going to the private sector," Mr Cullinane said.
"But it has to be said that this is a controversy entirely of the Department of Health's own making and the lack of transparency around this process has been absolutely shocking."
On Saturday, Tánaiste Leo Varadkare said no one in Government is satisfied with how Dr Holohan was given a state-funded role with Trinity College Dublin.
The secretary general at the Department of Health, Robert Watt, is expected to be invited before Public Accounts Committee to clarify the arrangement.
Tánaiste Leo Varadkar, says the decisions around Dr Holohan's new job which he's now turned down, need to be explained: "I am not sure what exactly happened and what processes went on.
"We are not satisfied with how it came about to be honest and that is why the Taoiseach is asking for a report to be done into it."