The junior education minister said he would favour Mr Coveney to take over as Taoiseach and Fine Gael leader when Enda Kenny steps down.
However, yesterday members of Fine Gael said his comments would not have any bearing on who becomes the next leader and pointed out that he is not a member of the party.
In an interview with Hot Press magazine, Mr Halligan said the Cork South Central TD “would be a good leader”.
“There are others too, but I’ve gotten to know him better than anyone else. I think he’s honest and upfront and I think he would do a good job.”
Reacting, Wexford TD Michael D’Arcy said: “He is entitled to his view but it’s not going to influence anybody. It’s a matter for the Fine Gael parliamentary party and the members of Fine Gael.”
This was echoed by Fine Gael TD Bernard Durkan who said his comments would not “affect anyone” in the party and suggested that Mr Halligan was only looking to gain attention at a quiet time of the year.
“It’s a good time to get a line or two or even three or four. But it would not raise any eyebrows. I would not take it too seriously.”
Mr Durkan added: “We live in a free country, people can comment on lots and lots of things.”
Dublin North West TD Noel Rock also brushed off the comments and said he didn’t see “any harm in it”.
“I think people are canny enough to make up their own minds in that respect. He doesn’t have a vote in the contest so he won’t have a material impact in it,” said Mr Rock.
Mr Halligan yesterday went on further to single out Mary Lou McDonald as his preferred candidate to lead Sinn Féin if Gerry Adams were to stand down.
It comes as financial accounts in the North have revealed that Sinn Féin is Northern Ireland’s top earning political party. The electoral commission which published the accounts that show that Sinn Féin had an income of £1.1m, while it spent £1.2m.
Mr Halligan said: “Probably Mary Lou will be the next leader and she is very articulate in the Dáil, she is a pretty good performer. I think she probably will lead Sinn Féin.”
Speaking on RTÉ’s Today with Sean O’Rourke programme yesterday Mr Halligan told Keelin Shanley that being part of the current partnership government has been “uncomfortable” for him: “Is it uncomfortable for me? Yes, it’s difficult for me but I felt as though I was obliged to do it. It’s uncomfortable because I can quite easily and rightly be criticised by people like yourself and others that I was on the backbench in opposition, left wing, criticising Fine Gael and the far right for not implementing policies that I thought would be best for the country.”