The NYPD is investigating an apparent break-in at the MTA’s Coney Island Yard after work crews discovered radios and other equipment missing from one of the subway system’s specialized work trains Monday morning, the Daily News has learned.

The equipment disappeared from one of NYC Transit’s four specialized “track geometry cars” while it was parked in the facility’s main overhaul shop.

The system’s diesel-powered track geometry cars carry an extensive suite of cameras, lights and measuring devices and make daily sojourns across the subway’s roughly 665 miles of track, making sure the rails are still aligned and in serviceable condition.

A source with knowledge of the situation told The News there was “all kinds of s–t missing” from the train, Track Geometry Car No. 4.

One source estimated the thief made off with thousands of dollars worth of handheld two-way radios.

In a statement to The News, MTA spokeswoman Kayla Shults characterized the missing gear as “standard maintenance items, including radios, an empty tool bag, and a safety vest” that were in a drawer on the train car.

The gear is not specific to the specialized nature of the track geometry car, she said.

The break-in likely occurred over the weekend. There were no obvious signs of forced entry and no indication that the train had been started or moved, sources said.

Sources confirmed that TGC4, as the burglarized car is known, was pulled off of scheduled inspection duty Monday pending police investigation.

MTA spokesman Tim Minton told The News that NYC Transit crews have tested the train and found no apparent damage. The train is slated to return to regularly scheduled track inspections as soon as possible.

Three of the four track geometry cars serve the broader subway system, while one car is assigned to the Staten Island Railway.

Subway yard security has been an ongoing challenge for NYC Transit, with a spate of break-ins since the start of the year linked to teenage vandals and joyriders.

It was not immediately clear if police suspect the weekend break-in is connected to any other acts of vandalism in recent months.