The State Pathologist's Office will not conduct autopsies at University Hospital Waterford's mortuary 'for the time being'.
Post-mortems needed during criminal investigations in the South East will now be carried out elsewhere.
Recent weeks have seen facilities at the mortuary come under scrutiny after four consultant pathologists at the hospital wrote to the HSE to say it was way over capacity.
Their letter stated: "Bodies decompose in the corridors, leading to closed-coffin funerals with relatives unable to view the remains as a result of gaseous decomposition.
"The trauma imposed on the bereaved is almost unspeakable".
In a statement today, the Department of Justice said: "In light of the concerns expressed by the consultant pathologists at University Hospital, Waterford, the Office of the State Pathologist has indicated that it has made arrangements for State forensic autopsies to take place in alternative facilities for the time being."
Sinn Féin called the news a 'very serious development'.
The party's Waterford TD David Cullinane said it's a "disgrace that it has come to this".
He added: “The HSE and the Department have very serious questions to answer. They must come before the Oireachtas Health Committee and we need a full, independent inquiry into services at the mortuary.”
"This is one I got wrong"
On Saturday, Taoiseach Leo Varadkar apologised for previous comments he made about the situation at the hospital.
He had faced sharp criticism after suggesting there was 'no evidence' to back up the consultants' claims.
In his Saturday statement, Mr Varadkar said: "I did not want to jump to conclusions or to side with one group of staff against another without knowing facts or before an investigation was carried out. That’s why I said that I did not know if the claims were true or not.
"Over the course of the week, corroborating statements have come to light and complaints have been made that I believe support the views expressed by the four consultants. This is one I got wrong.
"I want to apologise unreservedly to anyone who feels that I did not treat this issue with the seriousness or sensitivity it deserved."
Planning permission has already been approved for a new mortuary at the hospital, with temporary measures being put in place until that is completed.
