Speculation has mounted that Mr Cowen may not stand again after standing down as party leader last weekend.
He has so far refused to state his intentions, saying he needs time to reflect with family and friends.
Mr Cowen topped the poll in Laois-Offaly in the last election, pulling in a massive 19,000 votes and helping to elect running mates Sean Fleming and John Moloney.
Mr Fleming and colleagues were caught on open microphones in the Dáil yesterday discussing what would happen if Mr Cowen did not run.
“We’d be in fierce trouble,” Mr Fleming said.
With the Taoiseach on the ticket, “there’s a seat in the bag before we start, so then we’re fighting for the rest,” he said. But without the Taoiseach, “we’re fighting for the first seat”, Mr Fleming added.
His remarks came as the exodus of TDs from Fianna Fáil continued ahead of the election.
Noel Ahern and Ned O’Keeffe both announced they would retire from politics at the end of the Dáil term.
Another Fianna Fáil TD, Noel Treacy, confirmed that he would be unable to run on health grounds.
They bring to 17 the number of Fianna Fáil TDs who have announced they will not contest the election.
Mattie McGrath, meanwhile, resigned yesterday from Fianna Fáil and said he would contest the election as an Independent.
Announcing his decision, Mr McGrath claimed: “I didn’t leave Fianna Fáil, Fianna Fáil left me.”
Fianna Fáil had come to be associated with bankers and developers and a lack of regulation of the financial markets, he said, and had become disconnected from ordinary voters in the process.
“They’re seen as the party of the big fat-cats, and to hell with the small people,” Mr McGrath said.
He also claimed Mr Cowen had never taken his views on board since becoming Taoiseach, and the two men “never saw eye-to-eye”.
While yesterday’s news was not a major surprise as Mr McGrath had lost the party whip in the Dáil more than six months ago, the move is yet another blow to Fianna Fáil as the election draws near.
As it continues to lose TDs, the party is also under pressure to hold outstanding selection conventions in order to finalise its candidates for the election.
Because events of the last week dramatically shortened the life of the Government and meant the election will take place much sooner than originally anticipated, Fianna Fáil still have a number of conventions outstanding.
These are in Sligo-North Leitrim, Roscommon-South Leitrim, Donegal North East, Galway East, Mayo, Wexford and Mr Cowen’s constituency of Laois-Offaly.