He acknowledged anti-Semitism was on the rise in the country because of the economic crisis but said his government had a “zero-tolerance” towards it.
On Saturday the far-right Jobbik party held a protest against the Hungarian capital hosting the WJC meeting.
BBC reports that the party’s leaders regularly issue anti-Semitic statements.
The WJC usually hosts its assembly in Jerusalem, but chose Hungary this year to highlight what it says is growing anti-Semitism in Europe.
Addressing the opening session, Mr. Orban said: “Anti-Semitism is unacceptable and cannot be tolerated.”
He added that his government had a “moral duty to declare zero tolerance on anti-Semitism.”
However the WJC expressed its disappointment that Mr. Orban had not specifically talked about Jobbik, the third-largest party in parliament.
“The prime minister did not confront the true nature of the problem – the threat posed by the anti-Semites in general and by the extreme-right Jobbik party in particular,” it said in a statement.
The president of the WJC, Ronald Lauder, said Jews were again wondering if they were safe in Hungary.
Saturday’s rally by Jobbik was billed as a tribute to what organisers called the victims of Bolshevism and Zionism.