WASHINGTON — Three months ago, one of the CIA’s most experienced clandestine operatives started work inside the New York Police Department. His title is special assistant to the deputy commissioner of intelligence. On that much, everyone agrees.

In this Oct. 6, 2011, file photo, NYPD Commissioner Raymond Kelly listens during his testimony about NYPD intelligence operations to the New York City Council public safety committee in New York. Three months ago, one of the CIA’s most experienced clandestine operatives started work inside the New York Police Department. His title is special assistant to the deputy commissioner of intelligence. Since The Associated Press revealed the assignment in August, federal and city officials have offered differing explanations for why this CIA officer, a seasoned operative who handled foreign agents and ran complex operations in Jordan and Pakistan, was assigned to a municipal police department. Kelly said the CIA operative provides his officers "with information, usually coming from perhaps overseas." He said the CIA operative provides "technical information" to the NYPD but "doesn’t have access to any of our investigative files." (AP Photo/Bebeto Matthews, File) Exactly what he’s doing there, however, is much less clear.

Since The Associated Press revealed the assignment in August, federal and city officials have offered differing explanations for why this CIA officer — a seasoned operative who handled foreign agents and ran complex operations in Jordan and Pakistan — was assigned to a municipal police department. The CIA is prohibited from spying domestically, and its unusual partnership with the NYPD has troubled top lawmakers and prompted an internal investigation.

His role is important because the last time a CIA officer worked so closely with the NYPD, beginning in the months after the 9/11 attacks, he became the architect of aggressive police programs that monitored Muslim neighborhoods. With the earlier help from this CIA official, the police put entire communities under the microscope based on ethnicity rather allegations of wrongdoing, according to the AP investigation.

It was an extraordinary collaboration that at times troubled some senior CIA officials and may have stretched the bounds of how the CIA is legally allowed to operate in the United States.

The arrangement surrounding the newly arrived CIA officer has been portrayed differently than that of his predecessor. When first asked by the AP, a senior U.S. official described the posting as a sabbatical, a program aimed at giving the man in New York more management training.

Testifying at City Hall recently, New York Police Commissioner Raymond Kelly said the CIA operative provides his officers “with information, usually coming from perhaps overseas.” He said the CIA operative provides “technical information” to the NYPD but “doesn’t have access to any of our investigative files.”

CIA Director David Petraeus has described him as an adviser, someone who could ensure that information was being shared.

But the CIA already has someone with that job. At its large station in New York, a CIA liaison shares intelligence with the Joint Terrorism Task Force in New York, which has hundreds of NYPD detectives assigned to it. And the CIA did not explain how, if the officer doesn’t have access to NYPD files, he is getting management experience in a division built entirely around collecting domestic intelligence.

James Clapper, the director of national intelligence, mischaracterized him to Congress as an “embedded analyst” — his office later quietly said that was a mistake — and acknowledged it looked bad to have the CIA working so closely with a police department.

All of this has troubled lawmakers, including Democratic Sen. Dianne Feinstein, the chairwoman of the Senate Intelligence Committee, who has said the CIA has “no business or authority in domestic spying, or in advising the NYPD how to conduct local surveillance.”

Still, the undercover operative remains in New York while the agency’s inspector general investigates the CIA’s decade-long relationship with the NYPD. The CIA has asked the AP not to identify him because he remains a member of the clandestine service and his identity is classified.

The CIA’s deep ties to the NYPD began after the attacks of Sept. 11, 2001, when CIA Director George Tenet dispatched a veteran officer, Larry Sanchez, to New York, where he became the architect of the police department’s secret spying programs.

While still on the agency payroll, Sanchez, a CIA veteran who spent 15 years overseas in the former Soviet Union, South Asia, and the Middle East, instructed officers on the art of collecting information without attracting attention. He directed officers and reviewed case files.

Sometimes, officials said, intelligence collected from NYPD’s operations was passed informally to the CIA.

Sanchez also hand-picked an NYPD detective to attend the “Farm,” the CIA’s training facility where its officers are turned into operatives. The detective, who completed the course but failed to graduate, returned to the police department where he works today armed with the agency’s famed espionage skills.

Also while under Sanchez’s direction, documents show that the NYPD’s Cyber Intelligence Unit, which monitors domestic and foreign websites, also conducted training sessions for the CIA.

Sanchez was on the CIA payroll from 2002 to 2004 then took a temporary leave of absence from the CIA to become deputy to David Cohen, a former senior CIA officer who became head of the NYPD intelligence division just months after the 9/11 attacks.

In 2007, the CIA’s top official in New York complained to headquarters that Sanchez was wearing two hats, sometimes operating as an NYPD official, sometimes as a CIA officer. At headquarters, senior officials agreed and told Sanchez he had to choose.

He formally left the CIA, staying on at the NYPD until late 2010. He now works as a security consultant in the Persian Gulf region.

Sanchez’s departure left Cohen scrambling to find someone with operational experience who could replace him. He approached several former CIA colleagues about taking the job but they turned him down, according to people familiar with the situation who, like others interviewed for this story, spoke on condition of anonymity to discuss the department’s inner workings.

When they refused, Cohen persuaded the CIA to send the current operative to be his assistant.

He arrived with an impressive post-9/11 resume. He had been the station chief in Pakistan and then Jordan, two stations that served as focal points in the war on terror, according to current and former officials who worked with him. He also was in charge of the agency’s Counter Proliferation Division.

But he is no stranger to controversy. Former U.S. intelligence officials said he was nearly expelled from Pakistan after an incident during President George W. Bush’s first term. Pakistan became enraged after sharing intelligence with the U.S., only to learn that the CIA station chief passed that information to the British.

Then, while serving in Amman, the station chief was directly involved in an operation to kill al-Qaida’s then-No. 2, Ayman al-Zawahri. But the plan backfired badly. The key informant who promised to lead the CIA to al-Zawahiri was in fact a double agent working for al-Qaida.

At least one CIA officer saw problems in the case and warned the station chief but, as recounted in a new book “The Triple Agent” by Washington Post reporter Joby Warrick, the station chief decided to push ahead anyway.

The informant blew himself up at remote CIA base in Khost, Afghanistan, in December 2009. He managed to kill seven CIA employees, including the officer who had warned the station chief, and wound six others. Leon Panetta, the CIA director at the time, called it a systemic failure and decided no one person was at fault.