(AP) NEW YORK - In the fall of 2010, the FBI and New York Police Department were working together on a terrorism investigation on Long Island. The cyber case had been open for more than a year at the U.S. attorney's office in Brooklyn. So, the Justice Department was surprised when, without notice, the NYPD went to federal prosecutors in Manhattan and asked them to approve a search warrant in the case.
The top counterterrorism agent at the FBI in New York at the time, Greg Fowler, hit the roof. When two agencies don't coordinate, it increases the risk that the investigation and any prosecution could be compromised.
In an email response, Fowler prohibited his agents from sharing information with the NYPD's intelligence unit. He also suspended the weekly management meetings of the Joint Terrorism Task Force, the primary pipeline through which information flows to federal, state and local law enforcement agencies. It slowed to a trickle.
The episode was recalled by current and former NYPD and FBI officials who, like most who discussed this issue, spoke on condition of anonymity to describe sensitive law enforcement cases. It was not merely a low point in a relationship already littered with low points. It highlights how the dysfunctional partnership jeopardizes cases and sometimes national security.
The relationship between the FBI and the NYPD particularly the NYPD Intelligence Division is among the most studied collaborations in all law enforcement. In the New York media, the fighting and personalities are frequently covered like a dysfunctional celebrity marriage, with perceived betrayal and reconciliation spilling into the news.
The dispute is not trivial. At its core, it is based on fundamental disagreements between the nation's largest police force and the nation's premier counterterrorism agency. As the NYPD has transformed itself into one of the nation's most aggressive intelligence agencies and has spied on Muslims in ways that would be prohibited for the FBI, the rift has widened.
The result is that, in America's largest city, the NYPD and FBI are at times working at cross-purposes. Documents show that the NYPD conducted surveillance on mosques outside its jurisdiction, recording license plates of worshippers as they came and went. On its own, the NYPD has tried its hand at counterintelligence, the clandestine world that within the United States is run by the FBI under a presidential order.
The issue is especially relevant now following criticism from the top FBI agent in New Jersey, who said the NYPD's spying in his state had jeopardized national security because it made people afraid to cooperate with law enforcement.
"When people pull back cooperation, it creates additional risks, it creates blind spots," Michael Ward said. "It hinders our ability to have our finger on the pulse of what's going on around the state, and thus it causes problems."
The NYPD rejects that argument, and New York Mayor Michael Bloomberg has said his department will operate anywhere in the United States if it believes it's necessary to prevent terrorism.
"The police department can follow leads and threats wherever they come from," Bloomberg said, adding that it was all legal. "They can go into any state."
In the world of New York intelligence-gathering, there is perhaps no larger personality than David Cohen, the NYPD's irascible 69-year-old intelligence chief. Cohen was once one of the CIA's most senior analysts. To an analyst, one of the major pitfalls to be avoided is slipping into groupthink. When everyone endorses the conventional way of thinking, problems often arise.
Cohen similarly doesn't want the NYPD falling in line behind the FBI, according to those who have worked with him. The NYPD's lesson from the 9/11 terror attacks was that it could not trust counterterrorism to the federal government, so Cohen wants his team developing its own intelligence and chasing its own cases; if the FBI is doing the same thing, they eventually can combine their efforts.
Tensions between the FBI and local police are nothing new. Around the country, police grouse that the FBI snatches their biggest cases. The FBI complains that police don't alert the federal government early enough on big cases.
New York is supposed to be different. The NYPD is perhaps the premier police force in the nation. No other department comes close to the NYPD's manpower. No other city can rival its team of counterterrorism analysts, language capabilities or stable of officers working overseas.
New York was the first city to form a Joint Terrorism Task Force, a collaboration of federal and local agencies that has been replicated in cities nationwide. The NYPD has hundreds of officers assigned to that task force, working side by side with the FBI.
When the NYPD Intelligence Division, the secretive squad that answers to Cohen, and the FBI work together, they have produced strong cases. When the FBI was keeping tabs on two New Jersey men whose rhetoric was becoming increasingly violent, it was an undercover NYPD intelligence officer who helped make a case that sent the men to prison.
"They think their jurisdiction is the world. Their jurisdiction is New York City," New Jersey Gov. Chris Christie, the state's former top federal prosecutor, said recently. "My concern is this kind of obsession that the NYPD seems to have that they're the masters of the universe."
The NYPD's top lawyer, Andrew Schaffer, said New York police were not acting as police officers outside the city.
Police said they don't have to notify anyone of such operations.
"They don't exercise police power, they don't make arrests, they don't conduct searches, they don't execute search warrants," Schaffer told reporters recently. "That is beyond our power outside of our defined jurisdiction. But there's no prohibition on traveling to, residing in or investigating within the United States."
In May 2008, a young man named Abdel Hameed Shehadeh came to the attention of the NYPD as part of another investigation. Shehadeh, a former Staten Island resident, had become increasingly radicalized, according to court documents. That spring, he told a close friend about wanting to die as a martyr and wage violent jihad abroad against the U.S. military. He hoped to attend a terrorist training camp in Pakistan, authorities said.
The NYPD knew about Shehadeh. His friend was an NYPD informant.
But the FBI had no idea.
On June 13, the NYPD informant gave Shehadeh a ride to John F. Kennedy International Airport to catch a flight to Pakistan. The informant scrambled to notify the police, who alerted the FBI that a potentially dangerous man was about to fly to Pakistan.
The FBI suggested that the NYPD stop Shehadeh at the airport, current and former federal officials said, but the NYPD worried it would compromise the informant. With no justification for keeping him off the airplane, the FBI let Shehadeh fly but arranged for the Pakistani government to turn him away at the airport and send him home.
NYPD officials say they didn't intentionally withhold information from the FBI. They said they hadn't expected Shehadeh to move so quickly from talk to action. Once he did, police swiftly alerted the federal government. And there is nothing to prohibit the NYPD from starting its own investigations.
At the FBI, the incident reinforced the perception that the NYPD wasn't interested in a partnership. The strongest case the U.S. put together against Shehadeh focused on charges of lying to investigators. He faces up to eight years in prison.
At the NYPD, the FBI's concerns about the Shehadeh case are chalked up to the inevitable strains that sometimes occur in policing. NYPD officials promised to work more closely with the FBI, to share information earlier, federal and city officials said. FBI officials, too, promised to be more open about their cases. The goal was to make sure something like that didn't happen again.
In 2009, federal prosecutors in Boston charged Terak Mehanna in a terror plot. The Justice Department said he and his friends conspired to travel to Yemen for terrorism training so they could fight the U.S. in Iraq.
While Mehanna was in jail in Boston, a source working with the NYPD was in contact with Mehanna, according to current and former FBI and NYPD officials involved in the case. Such contact with another agency's suspect, who's already been charged, is considered improper.
The NYPD dispatched senior officials to Boston to explain to the Justice Department what happened, according to people briefed on the meeting. The NYPD said the contact with Mehanna was inadvertent, part of an unrelated investigation with clear New York ties.
The FBI asked, how could it be inadvertent when the NYPD was working 200 miles outside its jurisdiction?
In an interview last year, NYPD spokesman Paul Browne made a distinction between the NYPD "making contact" with Mehanna and "having contact" with him.
"We did not initiate any contact," Browne said.
He would not elaborate.
At trial, Mehanna's lawyers asked what the Justice Department knew about the NYPD's contact with Mehanna.
"We are not aware of any such contact," Assistant U.S. Attorney Aloke Chakravarty said.
Mehanna was convicted of terrorism charges in December and awaits sentencing. His lawyers said they still don't know how the NYPD was involved with their client.
As Cohen was expanding his department's counterterrorism mission, documents show that he also steered the NYPD into the murky world of counterintelligence.
Counterintelligence includes spying on other nation's spies inside the United States. Under a 1981 presidential order, that's supposed to be coordinated by the FBI. But as home to the United Nations, New York is a major arena for U.S. spy games.
In one highly unusual operation, the NYPD recruited a source close to the Iranian Mission at the United Nations, former senior NYPD officials said. Police had tried something similar before, former federal officials said, and crossed paths with the FBI. But this time, the FBI didn't know about it.
The Associated Press is withholding details of the operation for national security reasons.
Normally, agencies coordinate their efforts, a process known as deconfliction. Without it, two investigators might work the same source. One agency's informant might be the target of another agency's investigation. That can undermine cases and hurt both efforts.
Cohen's team recruited the source on its own, the former NYPD officials said.
The source gave the NYPD unique insight into the Iranian mission, a connection that the NYPD hoped would provide them early warning of Iranian collaborators in the city. But it also infringed on the turf of the FBI and the CIA, which have longstanding counterintelligence sources across the diplomatic terrain of New York City.
Cohen and Browne did not return several messages asking whether they had any comment or concerns about the AP reporting on this incident.
NYPD documents also show that police used one of its telephone pole-mounted video cameras to monitor the Saudi Mission, another sensitive diplomatic and counterintelligence location.
Documents also show that the NYPD began surveillance of Gholamzadeh Mahabadi Hossein, an Iranian man working closely with his country's U.N. Mission. Police believed he had technology expertise and ties to the Iranian Revolutionary Guard. Hossein was dubbed "Dasher."
Police put him under surveillance and trained a camera on his home in Queens, according to documents, as part of a secret police action dubbed "Operation Tailgate."
A former NYPD official familiar with Dasher said the NYPD was worried that people like him might be used as an Iranian proxy to launch an attack against New York.
The FBI, too, was well aware of Dasher, according to one former FBI official who worked the Iranian target at the time. To the FBI, Dasher was viewed as a potential spy, never a potential terrorist.
Had the NYPD raised Dasher's name with the Joint Terrorism Task Force, it would have flagged his ties to counterintelligence operations. That never happened.
Dasher has since left the country, officials said. There's no indication that he knew he was being watched. But officials said the incident is an example of how the broader mission the NYPD has taken for itself sometimes puts the department in lanes traditionally occupied by the FBI.
In Dasher's case, the FBI and NYPD were watching the same man. Neither knew what the other was up to.
FBI Director Robert Mueller said conflicts often arise between the bureau and local law enforcement.
"It is not unusual to have that," he recently told a Senate subcommittee. "And my belief is you sit down, you talk about it in private, you get it resolved and you move on."
In August, John Giacalone, a veteran FBI counterterrorism official with Long Island roots, arrived in New York to replace Fowler, who was promoted to run the FBI office in Portland, Ore. Giacalone knew about the FBI's problems with the intelligence division but said the relationship was a clean slate.
One of the first things the FBI did under Giacalone was to examine a terrorism case of the NYPD. It would become one of the most public spats between the FBI and NYPD. And it shows how, even when the two agencies collaborate, their efforts can be undermined by mutual distrust.
The NYPD had been using an informant to keep tabs on Jose Pimentel, a troubled young man whom authorities believed was being inspired to commit violence. But Pimentel had a drug problem and the informant used drugs with Pimentel, who had no known links to al Qaeda or other terrorism groups.
Under Fowler, the FBI said it was not interested in pursuing the case. But as new facts came to light, the FBI spent six weeks reviewing the case alongside the NYPD and city and federal prosecutors, federal officials said. The agencies agreed that Pimental was potentially dangerous and could not be ignored. They decided to move forward in state court, federal officials said.
The NYPD arrested Pimentel on Nov. 20. Authorities said he wanted to attack police and post offices using pipe bombs. Pimentel has since pleaded not guilty to rarely used state-level terrorism charges.
At a news conference, Bloomberg and New York Police Commissioner Raymond Kelly spoke to reporters.
"We had to act quickly yesterday because he was, in fact, putting this bomb together," Kelly said. "He was drilling holes and it would have been not appropriate for us to let him walk out the door with that bomb."
"There is an assessment process that is engaged in by the federal authorities, the U.S. attorney," Kelly replied. "We just believed we couldn't let it go any further. We had to act."
In an interview with the AP in late January, Giacalone said he had met with all the NYPD's senior leaders when he arrived in New York and found them to be "honest partners." Nothing has changed that view, he said.
Giacalone said the infighting has to end. Al Qaeda and its franchises might be crippled but they're still a threat. New York is still a target. To protect the city, the NYPD and FBI need each other.
"We are better working together than working apart," Giacalone said. "I am focusing on moving forward. We both recognize the way forward is to work together and to be good partners. The American people would never forgive us if our refusal to share intelligence resulted in a terrorist attack."