Edgar Bronfman, head of the World Jewish Congress, has written to European Commission President Romano Prodi asking for a "personal meeting", said the European body late on Wednesday.
He has sent an envoy to Brussels to pave the way for the meeting with Prodi, which he has asked should also be attended by Cobi Benatoff, president of the European Jewish Congress.
The two Jewish leaders this week accused Brussels of being "politically motivated" in withholding a report on violence against Jews and releasing an opinion poll that labelled Israel the biggest threat to world peace.
The envoy, Israel Singer, who is chairman of the Congress' executive council, will hold talks with Prodi early on Thursday in Brussels, said sources close to Prodi.
The European Commission has demanded a retraction of the accusations before a conference on the emotive issue can go ahead.
The seminar on ways to combat anti-Jewish feeling in Europe was due to take place next month, but was called off by the EU executive on Monday, after the Jewish leaders published an article accusing it of fostering anti-Semitism.
Edgar Bronfman, head of the World Jewish Congress, accused the European Commission of releasing "a flawed and dangerously inflammatory poll" of European public opinion that showed high mistrust of the Israeli government.
The Commission made clear its fury over the accusation in a coordinated series of comments and press statements, following a weekly meeting of the EU executive, where the issue was discussed at length.
Brussels took the unusual step of releasing Prodi's speaking notes to his colleagues, in which he called the accusation "defamatory".
"All commissioners expressed shock and disbelief at this attack on the Commission by these two organisations," said Prodi's spokesman, Reijo Kemppinen.
"This seminar cannot go ahead unless there is a visible change in attitude by these two organisations. In other words the ball is in their court," he said.
In an article in Monday's Financial Times, Bronfman and Benatoff said the Commission was guilty of fuelling anti-Semitism "by action and inaction".
It had released "a flawed and dangerously inflammatory poll" of European public opinion in November that showed high mistrust of the Israeli government, they said.
Kemppinen said the Commission had been at the forefront of anti-racism initiatives in Europe and that it "strongly rejects that legitimate criticism of actions by the government of Israel has anything to do with anti-Semitism".
Prodi has angrily denied he is an anti-Semite.
In his letter to Prodi, Bronfman wrote that the meeting was "important and even necessary" and expressed his deep appreciation for Prodi and his role as president of the Commission.
In his speaking notes, the Commission chief said he had received messages of support from other Jewish organisations including the Conference of European Rabbis and the Anti-Defamation League in the United States.