Ulster Unionist leader Mr David Trimble said yesterday he was perplexed by comments from a top aide to President Bush, who compared the IRA to al-Qaeda.
The comments by Mr Karl Rove, Mr Bush's chief strategist, also drew criticism from Irish lobbyists in the US.
Talking about the war on international terrorism, Mr Rove said in an interview: "This is going to be more like the conflict in Northern Ireland, where the Brits fought terrorism, and there's no sort of peace accord, with al-Qaeda saying, 'we surrender'."
Mr Trimble, who is attending the Republican National Convention in New York as a guest of the International Democrat Union, said he was confused by the comment.
"Al-Qaeda is quite a different terrorist organisation to those in Northern Ireland.
"It's perfectly reasonable, I suppose, to draw some parallel in that the war on terror will probably take a long time, just like it did in Northern Ireland, if that's what he meant," he told the Washington Post.
The Washington-based lobby group, the Irish National Caucus, said the comments were a sign of the "anti- Irish Catholic elements in the Republican Party" in the US.
Caucus president Mr Sean McManus said Mr Rove's statement "is, above all else, stupid, but it also may reveal the true colours of some anti-Irish Catholic elements in the Republican Party."
He added: "President Bush must immediately repudiate Rove's anti-Irish Catholic bigotry."