The Taoiseach, Mr Ahern, is expected to play down the possibility of a coalition between Fianna Fail and Sinn Féin after the next general election.
Concern has mounted among some Fianna Fáil TDs about the issue following remarks made by the Minister for Foreign Affairs, Mr Dermot Ahern, and a backbencher, Mr Ned O'Keeffe.
On Wednesday, the Minister for Foreign Affairs expressed his belief that Sinn Féin could become part of a government in the Republic quickly, if the IRA disarmed and disbanded.
Though many Fianna Fáil TDs are unhappy about Mr Ahern's comments they are prepared to accept them, believing that he was trying to encourage the Democratic Unionist Party.
However, Mr O'Keeffe's statement that he did not have a problem about Sinn Féin's links to the Provisional IRA has caused even more concern among his party colleagues.
"Dermot Ahern's comments were bad enough, but Ned's statement has put a whole different gloss on them," complained one Fianna Fáil TD last night.
The Taoiseach, who returned from an visit to Asia and the Middle East late last night, will speak at his party's Wolfe Tone commemoration in Bodenstown tomorrow.
He may choose to clarify the situation at this ceremony. "If not, there will be a desire on the part of many people that the situation is dealt with at the parliamentary party meeting," one TD said privately.
Dublin North West TD Mr Pat Carey said: "My belief is that this will cost us votes amongst middle-class voters and those who see FF as the guardians of republicanism."
Carlow/Kilkenny TD Mr John McGuinness said: "I would be concerned about [ Mr Dermot Ahern's] statement. An awful lot of the electorate have been irked by it." He told The Irish Times: "I think the Taoiseach has to make a clear statement now on the whole issue. The concern out there has to be dealt with".
Cork North Central TD Mr Billy Kelleher, who feared that the controversy this week had raised Sinn Féin's profile, said: "I don't think as a party that we should be putting up the white flag." The timing of the Minister's remarks has caused particular concern, since the Taoiseach had ruled out such an alliance with Sinn Féin just two weeks ago.
Dublin South West TD Mr John Curran said: "I think the remarks were a mistake. I think they will do us electoral damage."
Facing questions from Dr Jim McDaid, the Taoiseach said party policy had been decided three years ago, and nothing had changed. Describing Dr McDaid's intervention as "aggressive", one TD said: "He told the Taoiseach that he did not want any mumbling, that he wanted a straight answer for once."
Some TDs were relaxed about the remarks by the Minister for Foreign Affairs, while they were dismissive of those made by Mr O'Keeffe.
Laois/Offaly TD Mr Seán Fleming, who believed that there was no prospect of a coalition with Sinn Féin in the years ahead, said that party's policies would have to change.
Some TDs were reluctant to enter into the controversy, fearful that they could damage their prospects of getting transfers from eliminated Sinn Féin candidates in the next election.
Others remain unsure if the Minister for Foreign Affairs was "flying a kite" for the Taoiseach: "If I thought he was talking on his own, I would speak out. But I can't be sure that he isn't. There could be something going in the whole NI negotiations that we don't know about," one TD privately told The Irish Times.