He said the Government would continue to do its business but that there was a difference of opinion about whether or not he had asked ministers to resign in the knowledge the Green Party would not support him.
“The authority of my leadership remains but what was involved [on Thursday] was a refusal of the Green Party to support my entitlement and right as I saw it, based on the conventions that apply to coalition Governments, to put my team into the field for the fighting of this next election,” he said.
Mr Cowen was speaking after a meeting of the North South Ministerial Council in Armagh.
He said he the issue of the reshuffle, and the animosity it provoked within Fianna Fáil, had now passed and people had “moved onto the election”.
In Dublin Green Party leader John Gormley publicly contested the version of events put out by the Taoiseach and his Fianna Fáil colleagues.
Mr Gormley said the resignation of four additional ministers, in addition to Mary Harney and Micheál Martin, had to have been carefully orchestrated.
He said it was “stretching credulity” to suggest there was no conversation within the Government that the retiring ministers would step down together.
“You just don’t have everyone resigning at the same time,” he said.
Mr Gormley said he had been kept in the dark and was adamant the party had made it clear it was unhappy about the prospect of the reshuffle.
“I don’t think, frankly, people in the senior party could have been in any doubt about where I stood on the issue,” he told RTÉ’s Pat Kenny.
Yesterday morning the whips for the two coalition parties clashed over whether or not the Greens had indicated reluctant support for the promotion of six Fianna Fáil TDs to the Cabinet.
John Curran, the Government Chief Whip, said he had been at the meeting and the Green ministers never explicitly said they would vote down the appointment of new ministers.
His counterpart in the Greens, Trevor Sargent, said it had been very clear it had reservations about the reshuffle and had expected it to be brought up at Wednesday’s Cabinet meeting.
Meanwhile, one of the most outspoken of Mr Cowen’s critics, junior minister Conor Lenihan, put it up to the Taoiseach to shut him up.
He said that he would not make life easy for Mr Cowen by resigning from his post as Minister of State and that it was up to the Taoiseach to sack him.