The Sinn Féin leader has called for an independent investigation of the mortuary and post-mortem services at University Hospital Waterford.
It comes after the Taoiseach, Leo Varadkar, said there is no evidence to back up claims by four consultants that dead bodies were left decomposing on trolleys at the hospital.
Speaking in Waterford yesterday, Mr Varadkar also said that a new mortuary will be built at the hospital.
Mary Lou McDonald has accused the Taoiseach of displaying a "clear lack of empathy" and called on him to establish the facts before casting aside concerns raised by pathologists.
Labour leader Brendan Howlin also said that he was taken aback by the Taoiseach's comments.
"I happen to know some of the four senior consultants involved. They made that statement because they know it to be true," he said.
Mr Howlin said these consultants are working on the ground and the Taoiseach's dismissal of what they said was shocking and unacceptable.
This afternoon, Mr Varadkar said there is a dispute about what the true facts are.
Speaking after a meeting of the Cabinet in Cork, he said the only way to get to the bottom of it is through further investigation and that is being considered either by the Oireachtas Committee on Health or by HIQA.
Responding to Sinn Féin calls for a full independent investigation, he said: "The first thing you do when you carry out any sort of investigation, and HIQA can carry out an independent investigation, is to seek evidence to back up any claim.
"Just writing something in a letter or saying something isn't in itself proof or evidence," he added.
The Irish Hospital Consultants Association has said it is alarmed about the response from the Government to the concerns raised by consultants at the hospital.
The body, which represents over 90% of consultants working in hospitals here, said it is disappointing that the political response has been to question the validity of the concerns rather than to tackle the issue in a timely manner.