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A Muslim group, in collaboration with a Brooklyn imam once investigated as a possible co-conspirator in the 1993 World Trade Center bombing, paid $48,000 to run Islamic advertisements on the city's subway cars this September.

The ad campaign — known as the "Subway Project" — was designed to inform people about Islam and dispel common misconceptions about the religion, a representative for the Islamic Circle of North America told FOXNews.com. The story was first reported Monday in the New York Post.

But the effort to plaster 1,000 subway cars with pro-Islamic messages has given new life to the controversy that has surrounded the radical imam, Siraj Wahhaj, who is promoting the campaign.

Wahhaj was once listed by prosecutor Andy McCarthy as an unindicted person who may have been an alleged co-conspirator in the deadly 1993 terror bombing of the World Trade Center.

The imam appeared recently in a YouTube video praising the Subway Project's objective. In the video, Wahhaj says: "Every day in this city, some 4.9 million people ride the subways ... Imagine them seeing the word Muhammad. Imagine them seeing the word Islam ...This is one of the greatest projects I've ever seen."

Click here to see the video on YouTube.

In 1995, Wahhaj, a U.S.-born Muslim convert, provided supportive testimony for Omar Abdel-Rahman, the "blind sheik" who later received a life sentence for his role in the plot to blow up city landmarks.

"In time, this so-called democracy will crumble, and there will be nothing, and the only thing that will remain will be Islam," Wahhaj was quoted as saying in one of his sermons.

Aaron Donovan, spokesman for the state Metropolitan Transportation Authority, confirmed to FOXNews.com that the Islamic Circle had signed a contract to run the ads on 1,000 subway cars during the month of Ramadan.

When asked if the MTA knew of Wahhaj's background before signing the contract, Donovan declined to comment on the imam specifically.

"As part of the process, we review the ad and go to the Web site to make sure there is no inappropriate content and decided in this case there was not," he said.

Wahhaj told FOXNew.com on Monday that the group asked him to appear in their promotional video.

"I'm not the originator of this campaign," Wahhaj said. “I don’t want to distract from what this group is trying to do. My background is not a distraction, but people’s interpretation of my background might be a distraction.”

Wahhaj, who reportedly once called the FBI and CIA the "real terrorists," told FOXNew.com that he had no involvement in the 1993 World Trade Center bombing or in a plot to target New York City landmarks.

“Law enforcement has never come to me and asked me any questions about any of these allegations. I have never participated in any planning against this nation,” he said.

A representative of the Islamic Circle, who spoke on condition of anonymity, told FOXNews.com that the purpose of the campaign is not to convert people to Islam.

In response to questions about Wahhaj, the representative said, "Maybe he’s used some words that are creating some kind of misunderstanding, but he’s trying to create harmony and peace between people of different faiths.”

The black-and-white ads are set to come in pairs asking "Q: Prophet Muhammad?" or "Q: Islam?" with the answer "A: You deserve to know," according to the New York Post.

Subway riders curious to know more are encouraged to call a toll-free phone number or visit the organization's Web site, the Post reports.

Click here to read more from the New York Post.