The ad, sponsored by the pro-Israel American Freedom Defense Initiative, appeared after the Metropolitan Transit Authority lost a bid to refuse to post it on the grounds that it violated the agency's policy against demeaning language. In July, a federal judge ruled it was protected speech and ordered the MTA to place the posters.
The ad, featuring mostly black-and-white lettering on 117x72cm cardboard posters, will remain posted for a month, MTA spokeswoman Marjorie Anders said.
"In any war between the civilized man and the savage, support the civilized man," the ad reads. "Support Israel/Defeat Jihad."
Pamela Geller, executive director for the ad's sponsor group, rejected the MTA's assertion the posters were demeaning.
"There's nothing either hateful or false about my ad," Geller said in an email.
Despite the controversy, most subway riders who passed the ad in a tunnel at the Times Square station on Monday (local time) failed to notice it. Those who did were generally critical.
"Where is the protection of religion in America?" wondered Javerea Khan, 22, a Pakistani-born Muslim from the Bronx. "The word 'savage' really bothers the Muslim community. But it's hard for me to look at this poster and take it seriously."
Mel Moore, 29, a sports agent, said: "It's not right, but it's freedom of speech. To put it on a poster is just not right. But it caught my attention and I support freedom of speech, so you got to live with it."
Australian tourist Peter Johnson, 50, who had just visited the memorial to the September 11 hijack plane attacks, said he felt it was "a bit harsh to call someone a savage, but I do think that extremist Muslims seem happy to kill anyone regardless of their race or religion.
"I would have used the word 'barbaric.'"
Anders, the MTA spokeswoman, said the agency had not received any reports of vandalism against the posters.
The American Freedom Defense Initiative gained notoriety when it opposed creation of a Muslim community center near the site of the Twin Towers, which were destroyed in the September 11, 2001 attacks on the World Trade Center.
