Opposition leaders have called for an independent audit of the resources of the 18 congregations mentioned in the Ryan commission’s report to determine how much they can pay to victims of abuse in their institutions.
Fine Gael leader Enda Kenny said the congregations should not be allowed to make discretionary or voluntary contributions.
"Contributions should be agreed, they should not be discretionary or voluntary. Will you seek full recourse of their assets so you can understand what kind of contributions can be made?" he said.
Labour leader Eamon Gilmore said the Criminal Assets Bureau or the Revenue should be asked to carry out an independent audit of the congregations' assets.
"What happens if some of them don't make contributions and don't step up to the plate. What will the Government do then?" he asked.
Mr Gilmore also asked Mr Cowen whether the outcome of the negotiations would be brought before the Dáil to be considered. He said the court of public opinion "must be satisfied that the contributions are adequate."
The Taoiseach said he could not "legally impose" a solution on the congregations but said there was a "clear moral responsibility" on them to provide substantial additional contribution for the victims of abuse.
"I don't have a preconceived notion of what is adequate. Have to see their resources, they have to outline in a transparent way what their resources are," he said.
Mr Cowen said he had "no problem" bringing the outcome of the negotations before the Dáil for discussion.
He said he welcomed the fact that some congregations have confirmed their intention to make additional resources available to victims.
"I hope the others will reflect and come forward and make contributions commensurate with the assets at their disposal," he added. He said it was "very important" that they do so.