Dr Tony Holohan will step down from his role as Chief Medical Officer in July to join Trinity College as Professor of Public Health Strategy and Leadership on July 1.
However, in recent days, there has been major confusion over the appointment, specifically in relation to Dr Holohan's wage.
His salary is currently paid by the Department of Health, and it was widely believed that they would cease paying his salary once the career move is made in the summer.
Read more: What is Omicron XE? Symptoms of the new Covid variant thought to be 'most contagious yet'
The Chief Medical Officer receives €187,000 for his role as Chief Medical Officer, according to the HSE's most recent financial reports published last year.
However, crucially, Holohan will remain a civil servant after he steps down as CMO later this year.
His €187,000 a year public service salary will be paid by the Department of Health.
This was confirmed earlier this week by a Government minister.
Speaking to RTE Morning Ireland on Wednesday, Minister for Health Stephen Donnelly labelled the career change of Dr Holohan a "positive move" for the country.
Minister Donnelly defended the salary issue, saying that it wouldn't matter who is paying the wages of the new role.
"I think we're very lucky. Given his role and experience, he's a highly-employable individual. I think we're very lucky to have him leading this research"
When questioned by host Rachael English as to whether this meant that the department would be "paying for two CMOs", Minister Donnelly responded: "We're not. We need absolute clarity here
"There is one CMO, and there will be one CMO. What we have is the current CMO, who I think most people agree has done an outstanding job, he is stepping down as CMO and the department will be funding some of the most important health research that I think will be done in the coming years.
"If we break it down, let's say the department were to pay, or Trinity were to pay or they were to pay some each - it's all public money. It's a taxpayer-funded post. One of the details that's really important here is that he's not getting paid any more money."
Get breaking news to your inbox by signing up to our newsletter .
