The Fine Gael spokesman on justice said he could not understand why Mr Molloy embarked on a "crusade" relating to the Naughton case.
Mr Alan Shatter said it might be that it was presented to him before the trial that the man involved was innocently accused of horrendous offences.
"By the time the trial had taken place, there could be no excuse for him continuing to lobby on behalf of Patrick Naughton.
It is extraordinary that the former Minister of State saw fit, within days of Mr Naughton's conviction, to send a letter to the Minister for Justice, at the behest of the man's sister, to inquire whether this man could be given temporary release pending sentencing.
What thought did he have for the victim?"
He added that Mr O'Donoghue should accept that he was not a Minister with responsibility for justice if he did not know what was being done in his Department and if he was signing letters about whose contents he knew nothing.
The Labour leader, Mr Ruairí Quinn, said nobody liked to see a colleague in the House forced to resign from Government, but in the nature and extent of his representations Mr Molloy had made a serious error of judgment.
"I firmly believe that the Government's refusal to allow an independent investigation in this matter has a lot to do with the fact that the Minister's story simply does not add up," he remarked.
The public was entitled to the full story, not the partial version that was being prised out in dribs and drabs from the Minister, he added.
The leader of the Green Party, Mr Trevor Sargent, said it was shocking that what happened occurred despite Mr Molloy's 37 years as a TD and minister.