The officials spoke to the AP on condition of anonymity because they weren't authorized to speak publicly on the matter.
Jaji is in federal custody at an undisclosed location, a third law enforcement official said, also speaking on condition of anonymity because he was not authorized to discuss the case. Such an arrangement is common when a witness is cooperating in a sensitive investigation, but the official would not say whether Jaji is cooperating.
A federal prison Web site says Jaji was released on Jan. 22.
The FBI and U.S. Attorney's office in Brooklyn refused to discuss the case. Jaji's lawyer also declined to comment.
Jaji, 38, is the uncle of Najibullah Zazi, who was charged in September with plotting to attack New York City with homemade bombs. Zazi stayed at his uncle's suburban Denver home for several months last year.
Zazi bought beauty supplies in Colorado to make peroxide-based bombs, prosecutors have said. He tried to mix explosives in a hotel room in early September, then drove to New York to carry out an attack, possibly on the transit system, authorities said.
At the time of Zazi's arrest, Attorney General Eric Holder called the investigation one of the most serious terrorism cases since the Sept. 11, 2001, terror attacks, but few details about it have emerged since then.
The Denver Post reported in September that Jaji complained that his nephew had never paid him rent. But he also said it was "impossible" he could be a terrorist.
"He wants to become a citizen and bring his wife here from Pakistan," he told the newspaper.
The indictment was first reported Wednesday by The New York Times.
Two New Yorkers have also been charged in the case. The men, who attended a Queens high school with Zazi, were not directly linked to the foiled bomb plot. But authorities have said the two - Adis Medunjanin and Zarein Ahmedzay - traveled to Pakistan, where Zazi allegedly received training in explosives from al-Qaida.
All deny wrongdoing.
An indictment charged Medunjanin with receiving terror training and murder conspiracy. A federal prosecutor said he conspired to kill U.S. soldiers in Afghanistan after receiving military training from the terror network.
The government filed court papers last week alleging that during an FBI interrogation Medunjanin "made clear to the agents that he desired to cooperate with the government, and provided very detailed information about terrorist-related activities of himself and others in the United States and Pakistan. The papers did not describe the information.
Cab driver Ahmedzay, 24, has pleaded not guilty to charges that he lied to the FBI during the probe about places he visited during the 2008 trip.
Associated Press writer Matt Apuzzo contributed to this report.