"The question is how many refugees can a country accept. We have reached the end of our capacities," IKG president Oskar Deutsch told journalists in Vienna on Monday.
"Some of these so-called refugees will have grown up thinking anti-Semitism is normal," he said. "It would be terrible if this were to happen in Austria."
Austria has been a key country on the migrant trail and expects a record 95,000 applications for asylum this year and up to 130,000 in 2016, according to latest government figures.
Deutsch echoed comments made by the Central Council of Jews in Germany, which said it expected problems with integrating the mainly Muslim newcomers.
"Sooner or later we won't have a choice but to set an upper limit," the council's president Josef Schuster told Die Welt daily.
"Many of the refugees are fleeing the terror of the Islamic State and want to live in peace and freedom, but at the same time they come from cultures where hatred of Jews and intolerance are an integral part.
"Don't just think about the Jews, think about the equality between men and women, or dealing with homosexuals," he added.
German non-government group Pro Asyl criticised Schuster's comments, saying it was unfortunate the Jewish group was sharing the same position as the conservative Bavarian CSU party.
"It's disconcerting when the CSU and the Central Council of Jews are in fact demanding that we suspend the European Convention on Human Rights," said Pro Asyl's head Günter Burkhardt.