An imam who was scheduled to be sworn in Friday as the second Muslim chaplain in the New York Fire Department's history resigned that day after he made headlines for questioning whether 19 hijackers really were responsible for the Sept. 11, 2001, terror attacks (search), FOX News has confirmed.

The imam, Intikab Habib, had suggested a broader conspiracy may have brought down the World Trade Center, put a hole in the Pentagon and left about 3,000 people dead.

"The fire department this morning received the resignation of Imam Intikab Habib from his position as FDNY chaplain," the FDNY commissioner said in a statement Friday. "Based on comments he made to Newsday, Imam Intikab Habib would have been unable to effectively serve in the role he was appointed to."

An hour before Imam Intikab Habib was to be officially sworn in, Fire Commissioner Nicholas Scoppetta told reporters: "It became clear to him that he would have difficulty functioning as an FDNY chaplain. ... There has been no prior indication that he held those views."

In a telephone interview with Newsday Thursday, Habib, 30, a native of Guyana who studied Islam in Saudi Arabia, said he doubted the U.S. government's official story blaming 19 hijackers associated with Al Qaeda (search) and Usama bin Laden (search).

Click here to read the Newsday story on the interview.

Habib joined the department as chaplain on Aug. 15 after the FDNY's Islamic Society recommended him for the part-time position, which pays $18,000 a year.

His doubt apparently stemmed from video and news reports widely disseminated in the Muslim community.

"I've heard professionals say that nowhere ever in history did a steel building come down with fire alone," he told Newsday. "It takes two or three weeks to demolish a building like that. But it was pulled down in a couple of hours. Was it 19 hijackers who brought it down, or was it a conspiracy?"

He did say that the attack was a "tragic incident" and that he sympathizes with the families who lost loved ones.

"Whoever did it, it was a very wrong thing. It's always wrong to take an innocent human life," he said.

"It's sad," said Kevin James, a spokesman for the Islamic Society of Fire Department Personnel. "We had no idea those were his views. He's entitled to his opinion but he's not the right person for the chaplain."

And Mayor Michael Bloomberg spokesman Ed Skyler said: "The remarks were offensive and the mayor is satisfied that the chaplain has resigned."

Some have blamed the destruction of the trade center on a U.S. or Israeli plot designed to whip up support for attacks on Muslim countries. In 2003, New Jersey eliminated Amiri Baraka's position as poet laureate after he wrote a poem suggesting Israel had advance knowledge of the attacks.

The Associated Press contributed to this report.