Jewish groups are seeking to limit the damaging fallout from a controversial New York subway ad campaign that brands Muslims as “savages.”

Groups that work to build interfaith relations between Jews and Muslims are speaking out against the provocative ads, paid for by anti-Islamic activist Pamela Geller and the American Freedom Defense Initiative, that urge readers to “Support Israel. Defeat Jihad.”

A judge ordered the Metropolitan Transportation Authority to start running the ads in a small number of subway stations during the last week of September.

UPDATE: Several of the anti-Muslim blog posts were covered with stickers denouncing them as racist. Read Forward Thinking blog post.

“The challenge for us now is to raise our voices to say that these ads don’t represent and don’t reflect the mainstream American Jewish community,” said Mark Pelavin, senior adviser at the Union for Reform Judaism and associate director of the Religious Action Center.

Along with the pro-Israel message, the ad exhorts readers: “In any war between the civilized man and the savage, support the civilized man.”

The timing of the campaign could not be worse, as anger is still simmering worldwide over the anti-Islamic YouTube film “Innocence of Muslims,” which insults the Prophet Muhammad. Despite the small reach of the AFDI campaign – only 10 ads among the 11,000 spread across New York City’s 400-odd subway stations – the reaction to it is unpredictable.

Jewish advocates are particularly disturbed by the ads because they combine anti-Islamic propaganda and pro-Israel discourse as if supporting Israel and rejecting Islam were two sides of the same coin.

Rabbi Marc Schneier, president of the Foundation for Ethnic Understanding and a longtime champion of interreligious dialogue, told the Forward that he was “troubled” by the linking of Islam and Judaism in such a contentious way.

“People must understand that there is not a conflict between Muslims and Jews,” Schneier said. “The only conflict there is is between those who believe in coexistence and those who seek to destroy human rights.”

Schneier added that in the same way that other seemingly small manifestations against Islam have been taken as extremely offensive in the past, it would not be hard to imagine how this “could mutate in other parts of the Muslim world” — and raise anti-Israel feelings.

“These ads are Islamophobia at its worst, and in a very irresponsible fashion, since Israel has been brought into the frame,” Schneier said.

The MTA initially refused to run the ads, calling them “demeaning.” But U.S. District Court Judge Paul Engelmayer ruled that they constitute protected speech under the First Amendment. He specifically cited the pro-Israel perspective of the ads as evidence of their political character.

The New York office of the Anti-Defamation League released a statement in July, when the court decision against the MTA was first announced, referring to the campaign as “highly offensive and inflammatory.” The ADL, however, agreed with Engelmayer’s decision that the MTA had no right to block the ADS. Geller, who publishes a blog called Atlas Shrugs, called the judge’s order “a victory for the First Amendment” in an interview with Fox News, and said she didn’t think it would spark protests from Muslims.

San Francisco’s transportation authority agreed to run the same ads, but inserted a small white square next to each ad, stating that it “doesn’t support this message.” The MTA said such a disclaimer would violate its marketing policy.

Contact Andrea Palatnik at palatnik@forward.com