The Taoiseach denied in the Dáil this afternoon that the Government brokered a ceasefire deal with the "Real IRA".
It was reported in a Sunday newspaper last weekend that Mr Ahern's former special adviser, Dr Martin Mansergh, held secret ceasefire talks with the group through an intermediary, Belfast Redemptorist priest Fr Alex Reid, in aftermath of the Omagh bombing in 1998.
Mr Ahern dismissed the reports on Sunday. "It is very easy to make a full comment," he said. "There was no contact".
However, this afternoon he conceded in the Dáil today that the "Real IRA" had contacted Fr Reid, to act as a conduit for talks with the Government. Mr Ahern said Fr Reid had then consulted Dr Mansergh for advice.
"In subsequent meetings, [Fr Reid] took the opportunity to impress on them [the "Real IRA"] the need to stop and he reported on some of these observations to my special advisor and took advice from him," he said.
"I am entirely satisfied that Fr Reid, in all his contact, emphasised that regardless of a ceasefire, the Omagh bombers would be pursued."
Fine Gael leader Mr Enda Kenny had demanded a full explanation but said yesterday he accepted the Taoiseach's word there was no direct contact. The Green Party leader Mr Trevor Sargent also called for "a full statement".
The leader of the Labour Party, Mr Pat Rabbitte, today demanded full disclosure from the Government of the extent of its links with dissident republicans.
"At the very same time as the Dáil was being reconvened to put through emergency legislation to deal with the 'Real IRA', these contacts or indirect contacts were going on," he said.
"We need to have clarified once and for all what exactly was happening, what was the purpose of these contacts, what were their character, were they carried out at the behest of the Taoiseach or with his knowledge?"