The Minister for Foreign Affairs Dermot Ahern has had what he described as a number of "robust" exchanges with the Reverend Ian Paisley following the DUP leader's controversial weekend comments about President Mary McAleese.
Dr Paisley told his party's annual conference on Saturday: "I don't like the President of the Irish Republic . . . because she is dishonest".
He also said she hated Northern Ireland and accused her of breaching diplomatic protocol and being hostile to the PSNI.
At a meeting in Hillsborough Castle this afternoon, Mr Ahern told Dr Paisley his remarks were "unacceptable, unwarranted and untrue".
Mr Ahern confirmed to reporters after the meeting that the exchanges on the issue between him and Dr Paisley were "robust"
He said: "I indicated that I found it very unhelpful. I indicated that the Irish Government, none of the Government members would do likewise with any head of state - not least the Queen of England."
He added: "Those remarks which were unfortunate were made in the context of a party conference but I felt obliged on behalf of the Government and the Irish people to state quite clearly that we didn't accept them.
Earlier Dr Paisley said he stood over his remarks, claiming he had spoken the "truth" at his party's conference.
Dr Paisley said he defended his position when he met the Minister for Foreign Affairs this afternoon.
"He was told in no uncertain language that when she made remarks about Northern Ireland and called us unionists, Nazis they [the Government] were strangely silent," he said.
"I said you're not refuting anything I have said because you cannot. I have said the truth and you will just have to take it that those are the views that we're going to put forward," Dr Paisley said.
The DUP leader's comments were also dismissed by Northern Ireland Secretary Peter Hain.
"For my part, the Government holds President McAleese in very high regard," he said. "I saw for myself when she met the Queen only in December here at Hillsborough Castle that the Queen holds her in very high regard.
"I personally am a great admirer of hers and I think speaks for herself."
In a statement yesterday, the Taoiseach said no one had done more to reach out to all communities in the North. Áras an Uachtaráin was taken by surprise by the remarks but declined to comment officially.
There was controversy in January 2005 when, speaking on RTÉ radio, Mrs McAleese said of Nazis: "They gave to their children an irrational hatred of Jews, in the same way that people in Northern Ireland transmitted to their children, an irrational outrageous hatred, for example, of Catholics, in the same way that people give to their children, an irrational outrageous hatred of those who have different colour . . ."
Mrs McAleese apologised on RTÉ the following day.