The Minister for Arts, Sports and Tourism, Mr O'Donoghue, has denied he was trying to gag the Director of the National Museum by requesting he did not address the Dail committee discussing the controversial M3 road.
The chairman of the Oireachtas Committee on Environment & Local Government, Mr Sean Haughey, said ealier it was "very regrettable" Dr Pat Wallace would not be attending as he would have "a lot to say".
But Mr O'Donoghue said Dr Wallace had a statutory obligation to give his opinion on the motorway, planned in the vicinity of the historic Hill of Tara, to the Minister for the Environment, Mr Roche, before giving it to the committee.
The Green Party also complained about the absence from the hearings of Dr Wallace. Green TD Mr Ciaran Cuffe said: "I was hoping to ask Dr Wallace to comment on the archaeological importance of the Tara Skryne site and on the impact of the proposed motorway, but this opportunity has now been denied to myself and other members of the committee.
"I'm not convinced that the Director's statutory powers prevent him from speaking out.
"I can only conclude that this is a crude attempt to prevent further political embarrassment to the Government of the Hill of Tara debacle," Mr Cuffe said.
An Bord Pleanala granted permission for the building of the €680 million motorway, which goes through an archeologically important area near the Hill of Tara, last year.
The Hill of Tara has been described by a group of Irish historians and archaeologists as the "heart and soul of Ireland" whose name "invokes the spirit and mystique of our people".
Meanwhile, a protest group has claimed thousands of letters opposing the construction of the M3 near the Hill of Tara have been ignored by the Dail Transport Committee.
The Save Tara Skryne Valley Group said that 2,000 letters, including ones signed by musicians Shane MacGowan, Ronny Drew and David Kitt, were submitted.
According to the group's spokesman, Mr Vincent Salafia, none have had a response and none were given an opportunity to make further submissions.
The protest organisation said it has also been denied the opportunity to make a presentation to the Transport Committee, as its submissions were "beyond the terms of reference" for the committee.
A pro-motorway group, Meath Citizens for the M3, has made a presentation to the committee saying that more than 90 per cent of local residents were in favour of the current plans.
"This is completely undemocratic," Mr Salafia said. "We are appealing to Roisin Shortall and Senator David Norris, asking them to raise this matter in their next meeting."
The Save Tara Skyne Valley Group, which has collected 15,000 signatures on an Internet petition, has threatened to take legal action seeking an injunction against the building of the controversial motorway.