"We don't endorse the political views of Mr. Ben-Gvir," a spokesperson for the European Commission said on Monday ahead of the event.
The European Union's Delegation in Israel has cancelled its reception to mark Europe Day to prevent a far-right minister from doing a speech.
"The Delegation of the EU to Israel is looking forward to celebrating Europe Day on May 9 in its host country, as it does every year," the EU's diplomatic service, the EEAS, said in a statement on Monday afternoon.
"Regrettably, this year we have decided to cancel the usual diplomatic reception, as we do not want to offer a platform to someone whose views contradict the values the European Union stands for," it added.
EU delegations around the world will on Tuesday host events to celebrate Europe Day, which marks the anniversary of the 9 May 1950 Schuman declaration in which the creation of the European Coal and Steel Community was first proposed.
Ambassadors from member states as well as representatives of local governments are traditionally invited.
The invitation to the government by the EU delegation to Israel was over the weekend accepted by Ben-Gvir, the minister for national security and leader of the ultranationalist Otzma Yehudit party, whose six seats in the Knesset are propping up the government of Prime Minister Benjamin Netanyahu.
The announcement had stirred controversy with EU officials expressing unease at allowing Ben-Gvir to give a speech, as is customary.
A spokesperson for the European Commission had earlier on Monday told reporters that they were "consulting internally and also with our member states" on how to proceed.
"We don't endorse the political views of Mr. Ben-Gvir, we don't endorse the political views of his party because they are in stark contradiction with all the values and principles the European Union stands for and believes in," the spokesperson added.
Ben-Gvir, who has responsibility over the country's law enforcement agencies including the Border Police in the occupied West Bank, was in 2007 convicted for incitement to racism against Arabs and support for an organisation deemed a terrorist group by both Israel and the US.
Reacting to the cancellation, he said on Twitter that "it's a shame that the EU, which claims to represent multiculturalism instead practices silencing."
"Real friends know how to voice criticism and how to hear it as well," he added.
In a statement widely quoted by Israeli media, Ben-Gvir defended his right to deliver a speech over the weekend, writing that "Israel is a democracy, and in a democracy, one can hear different views."
The statement added that among the topics the minister wanted to raise was the EU and Israel's joint war on terrorism, and the necessity to strengthen cooperation in that fight.
The EU Delegation in Israel will however maintain its Europe Day cultural event for the Israeli public.