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NEW YORK – At the Federal Bureau of Investigation’s counterterrorism compound in Chelsea, a West Side neighborhood in New York City, the urgent announcement sends special agents rushing to the streets.

Has a secret terrorist cell been uncovered? A trove of bomb-making materials, perhaps?

The warning, it turns out, often concerns a matter far more mundane – even as it is universally alarming:

“If you’re parked on the south side of 18th Street, they’re towing cars.”

For decades, the FBI’s vehicles were off limits to New York City tow trucks, given the bureau’s authority. But over the past few years, the New York Police Department has towed hundreds of cars belonging to this and other governmental agencies. Not even police vehicles are exempt.

The cause of all this is a small towing unit of the NYPD’s Internal Affairs Bureau, charged with enforcing certain parking violations against government vehicles that might otherwise enjoy some latitude.

It does not matter if the offending car is a Ford Crown Victoria equipped with antennas from the hood to the trunk, or a federal government placard on the dashboard. The only thing that matters is whether the vehicle is parked in a no-standing zone in New York; if so, the Vehicle Enforcement Unit will tow it – no questions asked.

In 2013, the unit towed 1,855 vehicles that were illegally parked with a plaque displayed in the window, according to statistics provided by the Police Department.

Federal vehicles accounted for 311 of them; 361 were Police Department vehicles, and 242 belonged to the Fire Department.

No fines are typically paid, but dealing with the tows is nonetheless a time-consuming nuisance. Agents must first go to Police Headquarters in lower Manhattan to assert that the vehicles were being used on official business and then go to the tow pound to retrieve the vehicles.

“Technically, they were good tows,” said George Venizelos, the head of the FBI’s office in New York.

Venizelos said that the towing had “calmed down” in recent months and that he did not believe they were “harassment tows.”

Nonetheless, having a vehicle towed can often take four hours or more of an FBI agent’s time, distract several police officers from their regular duties and keep the unit from generating tow-related revenue for the city.

A police spokeswoman, Deputy Chief Kim Y. Royster, said: “We don’t just tow NYPD vehicles. We tow vehicles from all agencies – the Fire Department and federal agencies, too.”

Royster said the tows were for “safety hazard violations” that included being parked in bus stops, no-standing zones and elsewhere that parking was prohibited.

It is unclear whether the practice will continue under the new police commissioner, William J. Bratton. A senior police official said the commissioner was reviewing whether to disband Internal Affairs units that were devoted to pursuing low-level misconduct, a category that presumably includes parking abuses.

Special agents in New York generally receive a car from the federal government, often a Ford or a Chevrolet, for round-the-clock use.

Through a longstanding agreement, the Police Department issues parking placards to each agent: They come with considerable fine print and only limited parking privileges. They are not to be used to park in no-standing or no-stopping zones, in crosswalks or at bus stops. Nor are they to be used in the garment district during specified hours, among other limitations.

“It’s only been in the last two years where they’ve been actually towing the vehicles,” said Jon Adler, the president of the National Law Enforcement Officers Association.

Adler, who represents federal agents across the country, said that only in New York did the local authorities make a point of towing cars belonging to the federal government.

“This issue, unfortunately, is a recurring issue in New York City,” he said.