BCL university unit's Vice-President Rajibul Hasan on Friday evening lodged the case at Ashulia Police Station, OC Badrul Alam said.
The OC said the 16 people had been accused of attempt to murder and vandalism.
The two rival factions of the Chhatra League's JU unit clashed around 4:30am on Thursday.
At least 10 students, including BCL Bhashani Hall President Shakil Ahmed and member Rokanujjaman Sabuj, were injured.
Witnesses said BCL university unit Organising Secretary Nur Nabi and Bhashani Hall Secretary Aninda Baroi and their supporters were the first to attack Shakil’s supporters with sticks and sharp weapons.
They vandalised 25 rooms and stabbed Humayun, Shakil and Sabuj.
A meeting of the university Syndicate on Thursday night decided to suspend the 16 BCL activists.
It also launched an investigation into the incident. Anthropology Professor Rasheda Akhtar is heading a five-member probe team.