Officials say the move will save about $4 million a year at a time when revenues continue to decline amid the economic downturn.
The agency says it can call upon police helicopters in New York City and New Jersey during an emergency.
Port Authority PBA president Paul Nunziato says the agency is putting cost concerns ahead of public safety.
An in-house analysis found 228 of the 258 flights between August 2008 through April 2009 were patrols that found no unusual incidents. The remaining 30 flights included missing persons searches, business trips, photo shoots, memorial flyovers and tours.
The unit has three pilots, three mechanics, two maintenance supervisors and an operations agent.