An empty black prototype SUV left running for more than an hour caused a bomb scare on the Upper West Side around noon Sunday.

The bomb squad rushed to the BMW parked in front of the Museum of Natural History near the corner of West 77th Street and Central Park West, smashing two windows before realizing it was harmless, a NYPD spokesman said.

The vehicle's windows were blacked-out with a paisley pattern and the interior dashboard was blocked with a panel, raising the suspicions of police.

The owner of the car, a BMW employee testing a 2011 SUV prototype, arrived and eventually drove the vehicle away, said Tom Kowaleski, a BMW spokesman.

BMW adds the camouflage to prototypes to prevent competitors from stealing trademarked material, Kowaleski said.

As for why the car was left running, the employee apparently thought he had hit the off switch buried under the dashboard cover -- but the super-quiet engine didn’t let him know otherwise, he said.

advertisement | advertise on newsday

Two days earlier, police cleared a block of Times Square after investigating an unattended package. It was found to contain water bottles.

The investigations come in the wake of last weekend’s discovery of smoke coming from an SUV parked in Times Square; the vehicle, a 1993 Nissan, was found packed with potential explosives and its owner, Faisal Shahzad, a Pakistan-born U.S. citizen living in Connecticut, was arrested Monday night.