All of them were students of Hakimpur Qawmi Madrasa in Bagerhat Sadar upazila.
Mohammad Ali, offer-in-charge of Katakhali highway police station in Bagerhat, said when the CNG auto-rickshaw was returning to Hakimpur with the five madrasha students a truck from Mongla collided with it around 12:00am, leaving three students dead on the spot.
Two injured students were taken to a hospital.
The driver managed to flee with the truck after the accident.
The bodies were recovered and taken to the highway police station, he said.