The questions on the ads aren't subtle: Leaving Islam? Fatwa on your head? Is your family threatening you?
A conservative activist and the organisations she leads have paid several thousand dollars for the ads to run on at least 30 city buses for a month.
They point to a website called RefugefromIslam.com, which offers information to those wishing to leave Islam, but some Muslims are calling the ads a smoke screen for an anti-Muslim agenda.
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Pamela Geller, who leads an organisation called Stop Islamisation of America, said the ads were meant to help provide resources for Muslims who are fearful of leaving the faith.
"It's not offensive to Muslims, it's religious freedom," she said.
"It's not targeted at practicing Muslims. It doesn't say 'leave,' it says 'leaving' with a question mark."
'Anti-Muslim bigotry'
She said the ads cost about US$8,000 (AU$9,692), contributed by the readers of her blog, Atlas Shrugs, and other websites.
Similar ads have run on buses in Miami, and she said others were planned for more cities.
Faiza Ali, of the New York chapter of the Council on American-Islamic Relations, said the ads were based on a false premise that people face coercion to remain with Islam.
She said Muslims believe faith that is forced is not true belief.
"Geller is free to say what she likes just as concerned community members are free to criticise her motives," Ali said.
Geller has a history of speaking out against Muslims, and the ads are "a smoke screen to advance her long-standing history of anti-Muslim bigotry," Ali said.
Geller said she had no problem with Muslims, but was working to "maintain the separation of mosque and state".
Adverts 'within guidelines'
She is also among those speaking out against the building of a mosque and cultural centre near ground zero.
The Metropolitan Transportation Authority said the ads have been in place since May 14 and were scheduled to come down in a couple of weeks.
There are about 6,000 buses in the MTA fleet.
MTA spokesman Aaron Donovan said all ads are screened. Most are reviewed by the company that handles the MTA's advertising opportunities, but some are sent to the MTA for ultimate approval.
Geller's ad was sent to the MTA for assessment, he said.
"We reviewed it and found that it did not violate the MTA's ad guidelines," he said.
The agency had received no complaints since the ads went up, Donovan said.
The 30 or so buses with the ads pass through all five boroughs of the city.
