"We will discuss frankly and openly about some specific issues which are of our mutual concern," EU foreign policy chief Josep Borrell said at the start of the meeting in Brussels.
"I am talking about the situation in the Palestinian territories and the Middle East peace process which is stalled."
Israeli Prime Minister Yair Lapid dialled in remotely for the EU-Israel Association Council talks. The country's travelling delegation was headed by intelligence minister Elazar Stern.
Council meetings have been suspended for a decade since Israel ditched them over the EU's opposition to expanding settlements in the West Bank.
The EU has been looking for a fresh start with Israel since right-wing leader Benjamin Netanyahu was ousted from office in 2021 after 12 years in charge.
"All in all, today is a good occasion to show our determination to have a positive and fruitful relationship with Israel, pushing for peace," Mr Borrell said.
He said support expressed by Mr Lapid in a speech at the UN for a two-state solution with the Palestinians was "very important".
"We want the resumption of a political process that can lead to a two-state solution and a comprehensive regional peace," Mr Borrell said.
But he said a UN report on the situation in the occupied territories was "worrisome" as the number of Palestinians reportedly killed this year reached the highest level since 2007.
Another bone of contention between the two sides is Israel's firm opposition to EU-mediated efforts to revive the 2015 nuclear deal with Iran.
"Well, this is one of the issues in which certainly we disagree," Mr Borrell said.
"For the time being in any case, those (nuclear deal) negotiations are stalled."