The latest terrorism arrests in New York were announced with the fanfare of a City Hall news conference, a dramatic photo of a broad daylight takedown by the police department and reassurance from local law enforcement officials that a serious threat had been neutralized.

Only one thing was missing: the FBI.

The FBI’s glaring absence at the announcement and silence since then about the arrests of two men described by police as raving anti-Semites and would-be jihadists bent on attacking a synagogue raised questions Friday about the severity of the threat and the strength of the case.

 The FBI and the Department of Justice have declined to explain the New York Police Department’s assertion that the FBI-led Joint Terrorism Task Force, always a central player in past terror cases, was made aware of the investigation but decided not to get involved. And the U.S. Attorney’s office in Manhattan, known for its successful prosecution of several high-profile terror cases for nearly two decades, also declined to comment.

But a law enforcement official briefed on the case said Friday that the FBI backed away because it had “reservations” about how it was conducted by the NYPD’s Intelligence Division. The FBI also concluded it “wasn’t a legitimate terrorism case,” said the person, who wasn’t authorized to speak publicly and spoke on condition of anonymity.

In the past, federal authorities have expressed concern about the Intelligence Division’s tactics and its use of a cadre of undercover investigators like one used in the synagogue case.

The NYPD’s top spokesman, Paul Browne, said Friday that any doubts about the investigation are unwarranted.

“When someone acquires weapons and plans to bomb the largest synagogue in Manhattan he can find, what do you call it? Mischief?” he said.

Rather than seek the usual federal conspiracy charges, the NYPD worked with the Manhattan district attorney’s office to bring a case under an obscure state terrorism law that the office had never used before and that was viewed as symbolic when it was signed only six days after the Sept. 11, 2001, attacks. The case has been turned over to the office’s Investigation Division, which has a history of prosecuting racketeering, cybercrime and money laundering cases — not terrorism.

Police Commissioner Raymond Kelly said Thursday that there was no evidence that the suspects, Ahmed Ferhani and Mohamed Mamdouh, were linked to al-Qaida or any other terrorist organization. But officials insisted the men posed a dire danger that had to be dealt with however possible.

READ MORE: NBC NEW YORK