Chair of the Oireachtas Finance Committee says it will be seeking information around the process behind Tony Holohan's new role.
John McGuinness was speaking as the outgoing Chief Medical Officer is leaving his post to take up a position with Trinity College Dublin (TCD).
However the change is an open-ended secondment, rather than a permanent move.
As such the Department of Health is to continue paying his salary of more than €187,000 - even though he will not be working there.
Dr Holohan himself has said he has no plans to return to his role as CMO at any point in the future.
But Deputy McGuinness told The Hard Shoulder the Secretary-General of the Department of Health should appear before the committee.
"I think it's the department and Robert Watt that should be before the committee explaining everything.
"Indeed on the Committee for Finance and Public Expenditure and Reform, we deal with issues like this.
"We will be seeking the information that's now required to clarify matters for the general public.
"And hopefully to put in place a better process that will attract whoever is interested in the job - and maybe someone from outside the civil service.
"And that people will have more confidence then in the system that we have".
'Less than transparent'
He says decisions are being quietly made by a small number of people.
"The fact of the matter is that this is a mess and it has been less than transparent in relation to the process that led to Tony Holohan getting this position.
"I believe now what's needed is an open and detail of exactly who made the decision in relation to this, how it started, and who sanctioned it.
"There are far too many of these decisions being made quietly by a small number of civil servants and senior politicians - and it's not the way to do business.
"I've great respect for Tony Holohan, and admiration for him as the public would have, but it's not about him - it's about the process".
Deputy McGuinness says more information has to be given by the Department of Health.
"Someone within the department made the decision, someone started the process to consider this and finally make that decision.
"It's clear from the [Health] Minister's interviews that he wasn't party to that, that he didn't know anything about it.
"The Taoiseach didn't know anything about it, the Tánaiste didn't know anything about it: and that is no way to run a government, it is no way to run the civil service.
"And thereafter, when it was publicly known that Tony Holohan was taking up this new position, the department refused to give a detailed account of the process and of the person who signed off at the end of this.
"So what we need to do is we need to find out what that process is, we need to investigate it, to understand it.
"The public are quite cynical about politics, and this has not gone down well".