The men shot on Route 16 just after 2 a.m. Friday were taken to the hospital with what were described as non-life threatening injuries.
Their names were not immediately released.
A department spokesman says the unnamed trooper attempted to pull over the vehicle for traffic infractions. Those infractions were not specified, but police say they expect to charge the men.
Per protocol, the trooper has been put on paid leave pending the investigation.
Police are urging commuters to seek alternate routes Friday morning.