The incident happened around 3:00 a.m. on Route 676 southbound just past the Atlantic Avenue exit.
The troopers were investigating an accident where a driver lost control of a car and struck the median on the highway.
A second vehicle traveling southbound hit the police cruiser while the troopers were still inside, officers say.
The troopers were taken to Cooper University Hospital with non-life threatening injuries.
So far, there is no word on whether charges will be filed against the driver.