Simon Coveney said he had a 'constructive and frank' meeting with the Israeli PM in Jerusalem
The Israeli Prime Minister has accused Ireland of supporting non-governmental organisations (NGOs) who want to "destroy" his country.
Benjamin Netanyahu made the comments to Foreign Affairs Minister Simon Coveney in a meeting in Jerusalem earlier.
The Prime Minister criticised Ireland's 'traditional stance' on the Israeli-Palestinian conflict.
In a statement after the meeting, Mr Netanyahu's office said: "Prime Minister Netanyahu expressed his dissatisfaction over Ireland's traditional stance and told the Foreign Minister that his country does not condemn Palestinians for incitement and for glorifying those who commit terrorist attacks.
"The Prime Minister also asked him why Ireland helps NGOs that call for the destruction of Israel and noted that many European countries are overlooking the core problem of the conflict – the Palestinian refusal to recognize the state of the Jews."
Minister Coveney, meanwhile, struck a more diplomatic note in his account of the 'constructive and frank' meeting.
He explained: "Of course, we have clear differences on some issues, but these differences are honestly held and openly expressed.
"Our discussions touched on a range of issues, including settlements, the humanitarian and political situation in Gaza and, more broadly, the prospects for the resumption of meaningful negotiations in the Middle East Peace Process."
Minister Coveney said he made clear "the level of public and political interest in these issues in Ireland", and added they also discussed bilateral issues such as "the healthy and growing trade" between the two countries.
As part of his three-day visit to the Middle East, Minister Coveney is also scheduled to meet with Palestinian leadership - including President Mahmoud Abbas - in Ramallah on Thursday.