Minister for Foreign Affairs, Mr Cowen, today criticised the security barrier that Israel is building in the West Bank.
His remarks during a visit to the country were seen as serving notice that the new leadership of the European Union is likely to put more pressure on the Israeli government than its predecessor.
In a speech at Tel Aviv University, Mr Cowen said that European criticisms of Israeli policy do not stem from hostility against Israel.
He called on the Palestinian Authority to create a "law abiding society" and to take measures to eliminate corruption.
Mr Cowen also urged the two sides to resume negotiations on the internationally backed "road map" peace plan.
His criticism of the Israeli barrier was in sharp contrast to the generally pro-Israeli tone set by the Italian government, which held the EU's rotating presidency until Ireland took it over January 1st.
Mr Cowen's remarks came only weeks before the International Court of Justice in the Hague is to examine the barrier's legality at the request of the Palestinians.
He said the EU had not taken a position on the barrier case but emphasised it was unhappy that sections of the partially completed complex of fences, ditches and razor wire slice deep into the West Bank.
"From the Palestinian perspective, (the barrier) understandably appears to be an attempt to redraw the 1967 frontiers," he said.