But the government decided against giving him protection, and Mr. Vinas, 35, has found himself unexpectedly back in New York, where he was raised and converted to Islam more than a decade ago. The F.B.I. and the Justice Department declined to comment, but a senior government official said there were concerns about whether Mr. Vinas would adapt to the program and potential conflicts with law enforcement officials who administer the witness protection program.

Nonetheless, the decision could affect future government cases as defense lawyers weigh whether to help prosecutors. The F.B.I. and federal prosecutors have long relied on informants to build cases against mob bosses, crooked Wall Street traders and drug dealers, and current and former law enforcement officials questioned whether potential cooperators would decline to help the government without a guarantee of safety in return.

“How often do you get an American who went into Al Qaeda?” asked Jack Cloonan, a former F.B.I. agent who investigated the group. “I would think you would want to do everything you could for him. If I were the agent, I would be hard-pressed to accept this.”

In a series of interviews, his first since being freed, Mr. Vinas gave an unusually revealing look at life inside Al Qaeda. He spoke of a training camp, where he slept in flea-ridden sleeping bags but befriended other young men from around the world, and gained access to Qaeda leaders, who discussed with him the most effective ways to cause mass destruction inside the United States. He suggested blowing up the Long Island Rail Road, or a Walmart.

Mr. Vinas became interested in Islam before the Sept. 11 attacks after meeting a Muslim woman at a mall. He converted in 2004 at a mosque in Queens, did odd jobs in New York and eventually fell under the spell of Anwar al-Awlaki, a radical cleric and Qaeda recruiter in Yemen whose YouTube videos were popular among Islamic extremists.