The incident - which flew in the face of assertions by Mayor Bloomberg and other officials that the had gone well - happened just outside the Bowling Green subway station.
One source familiar with the incident said a transit cop grabbed a firefighter from Squad 18 without any provocation as the firefighter tried to walk into the station.
The cop threw the firefighter to the ground, according to the source.
The victim landed on his air-supply pack, which was strapped to his back.
Firefighters who witnessed the scene confronted the police officer, asking why he had grabbed their colleague.
"I had to do it," said the cop, according to the source, who said that incredulous firefighters then reminded the officer that the exercise was only a drill, not a real emergency.
The firefighter was not injured, and walked away from the scene.
The cop apparently was acting on the belief that firefighters were barred from the station while police searched for a simulated explosive device, the source said.
The source noted that cops and firefighters had been allowed inside earlier, but almost everyone was eventually told to leave because another "bomb" was suspected.
At that point, only the police bomb squad was supposed to be there.
That's when the grabbing incident took place, even though cops not assigned to the bomb squad were in the subway station at the time, the source said.
The NYPD said it had no record of the incident, and an FDNY spokesman declined to comment.
But a source said the incident had been written up, with the names of those involved, for FDNY officials.
The violence came on the heels of a decision last week by the Bloomberg administration to clearly spell out which agencies have command at the scene of various types of emergencies, an issue that has been a sore point for FDNY-NYPD relations.
Yesterday's exercise involved police, fire, and other agencies confronting a mock double bombing and collision of two subway trains at the station.
The drill involved more than 1,000 local, state and federal personnel.
"People arrived, people communicated, people found the simulated bomb," Bloomberg said after the drill. "They removed the simulated injured people. It was good exercise."
Emergency Management Commissioner Joseph Bruno said, "We've learned that the agencies coordinate very well. We've learned that they responded very, very promptly."