Secretary General of the Department of Health Robert Watt said a new permanent Chief Medical Officer will be appointed over the next few months.
He told the Oireachtas Committee on Health that this will be done based on an open competition.
Outgoing Chief Medical Officer Dr Tony Holohan announced last month that he is stepping down from his position as CMO to take on a new role as Professor of Public Health Strategy and Leadership at TCD.
Mr Watt said Dr Holohan is hoping to contribute very significantly in his new role on public health policy and his contract is of indefinite duration.
Fine Gael senator Martin Conway said this means the Department of Health could be funding it for the next 20 years and that it was "highly inappropriate".
Sinn Féin's health spokesperson David Cullinane said the new post being taken by Dr Holohan would be really good for Trinity and the State, but if he is still paid by the Department of Health, it can be problematic as a secondment means that a person can return to their post.
Mr Cullinane said it raises questions for the department to answer including who signed off on it.
Earlier, Minister for Health Stephen Donnelly said the secondment of Dr Holohan to the TCD role is "really positive", and a move that the country will benefit from.
Speaking on RTÉ's Morning Ireland, Minister Donnelly said Dr Holohan will be leading national research on pandemic preparedness, which "he is uniquely qualified to do".
He said that he was fully supportive of the move and it mirrored what Asian countries did after the SARS outbreak in order to be better prepared for future similar events.
The minister said: "He'll be organising collaborations across universities with the World Health Organization and with the EU ... it's incredibly important work.
"The department would have been paying for him within the department anyway so, ultimately the winners out of this are the State, in that we have someone with his experience who can lead this work."
Mr Donnelly said he did not sign off on the secondment of Dr Holohan but he fully supports it.
"I think we're very lucky to have him leading this research," he said.
There is a very close collaboration between healthcare and academia in Ireland, he said, and there are consultants in many hospitals who also have academic posts and are involved in research and training new clinicians.
Yesterday, the Taoiseach told the Dáil that he had "no hand, act or part" in the secondment of Dr Holohan.
A TCD spokesperson confirmed that the role will be "funded by the Department of Health ... under the same terms and conditions of his existing contract".
The spokesperson added: "Secondments between organisations are a regular and common feature across the civil and public service to encourage inter-departmental and inter-agency cooperation and the sharing of knowledge and skills in the public interest."
The TCD role was not put out to open competition and the university said it "was created with Dr Holohan in mind".
It was created by the college board in the context of recent and ongoing global events, including conflict, climate change, migration and the recent pandemic.
Additional reporting Paul Cunningham and Fergal Bowers
