At the Alpbach political forum in Tyrol on Sunday, the Austrian president said that not all criticism of Israel should be "raised to the level of anti-Semitism", but he added that anti-Semitism in Europe in any form needed to be rejected.
The Austrian-Israeli Society (ÖIG) has expressed dismay over Fischer's comments - saying that he had shown a "biased attitude".
The president, who was usually so concerned about Austria's neutrality, did not attempt to be neutral at all, said an ÖIG statement.
ÖIG president Richard Schmitz said it was Israel's right to defend itself against air strikes from the Gaza Strip.
Fischer had no right to question this, said Schmitz, or compare it to the aggression of Hamas, the radical Islamist movement that dominates Gaza.
Fischer said that the current developments made the conflict between Israel and the Palestinians "even more difficult to solve". He added that violence only increased hatred, and posed the question of whether a policy of violence fuelled terrorism rather than fighting it.
EU High Representative for Foreign Affairs Catherine Ashton was also present at the talks in Alpbach. She reminded listeners about the "enormous humanitarian challenges" in the Gaza strip.
A sustainable solution for peace needed to be found for the Middle Eastern conflict, said Ashton, and a two-state solution was necessary so that Israel and Palestinians could live peacefully together.