Authorities say the two officers saw the group smoking as they entered the Freeman Street train station in Crotona Park around 2:30 p.m.
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When the officers asked the group to put out their cigarettes, they refused.
As the officers were removing them from the station, the group fought back.
Two suspects were arrested at the scene, but a third got away and is being sought by investigators.
"People are now going to jail and having to spend time fighting a case instead of just complying," said NYPD Chief of Department Jeffrey Maddrey. "This should not be happening."
The assault happened just two days after an NYPD lieutenant was slashed with a boxcutter as he was responding to a fight at the 238th Street station in Kingsbridge.
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There have been more than 3,200 assaults on NYPD officers so far this year.
Over the last two years, the total number of assaults have increased by 20%.
"If you took out the assaults on law enforcement just in transit, our transit assaults would be way down," said Maddrey.
Though assault on police officers carry stiff penalties - the recent incidents show they are apparently not a deterrent.
"This is the second in a week," said Professor David Sarni at John Jay College of Criminal Justice. "We really have to see when the defendants commit these acts, they must be held accountable."
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Two of the men arrested in Monday's incident have been charged with assault charges.
MORE NEWS: 2 arrested after NYPD lieutenant allegedly slashed with box cutter while responding to fight at Bronx subway station
Footage reveals NYPD lieutenant attacked on subway
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