Sources have revealed to the Herald that Mr Cowen was "extremely contrite" when he was faced down by ministers after his infamous Morning Ireland interview.
It was during discussions with his Cabinet colleagues at the breakfast on Wednesday morning that he decided a public apology would be necessary to dampen the issue.
Mr Cowen is said to be totally embarrassed by the fallout from the interview that Fine Gael's Simon Coveney alleged sounded "halfway between drunk and hung over".
Despite the apology, a rump of backbenchers are unhappy with Mr Cowen's response and are holding talks behind the scenes. They want Micheal Martin, Dermot Ahern or Mary Hanafin to lead a revolt, but for the moment none of those are willing to make a move.
The Green Party eventually admitted today that the Taoiseach had given a "poor performance" after maintaining silence since Tuesday.
The party's chairman Dan Boyle said: "I think it's been acknowledged that it was a disappointing performance, a poor performance."
He said that the junior coalition partners had been "letting things play out".
"We acknowledge the apology that was made and our preference is that we have our own think-in this week and we want to deal with things," he said.
His party colleague, Communications Minister Eamon Ryan, described the incident as "very unfortunate".
But former Fianna Fail minister Willie O'Dea defended Mr Cowen and followed the party line of try to divert blame onto Mr Coveney.
"He has to bond with his party. What better way to do it than after a day's solid work? He is a very good man at a social occasion," he said on Newstalk's Breakfast Show.
"It wasn't his best performance. I was a bit surprised at the extent of the reaction. I think it was triggered by Simon Coveney."
However, with the Taoiseach unable to quell upset over his think-in antics, Fine Gael last night revealed that they have speeded up the process of selecting their election candidates.
Labour blamed the international bad press for causing a spike in interest rates on the bond markets.
Party leader Eamon Gilmore said that it was time to clear the air and the "one good thing" the Taoiseach could do for the country was call an election.