The fracas began after the film's screening ended late in the evening, and students from ABVP fought with activists of Left-backed student unions in which a few of them received minor injuries, officials said.
Agnihotri faced black flags at the campus gates, sloganeering and placards bearing message that asked him to leave.
The filmmaker claimed he was "manhandled and gheraoed" by some students and even the glass pane of his car was left shattered in the commotion.
"We all know Kher's views in the whole debate on whatever happened in JNU. He is acting in this film which has divisive content. We are protesting against that," Sounak Mukherjee, a first year MA student of English Department, said.
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"The students had isolated four of them inside the campus following the incident. I have handed them to the police. There were some outsiders also. The students said they molested some girls," University Vice Chancellor Suranjan Das told PTI late tonight.
BJP leader Roopa Ganguly also rushed to the campus but was stopped at the gate by the police.
The state-run varsity's alumni association, which runs the Triguna Sen auditorium, had decided to cancel the booking for a pre-release screening of the film in their hall.
The producers, however, went ahead with the screening at an open-air space in the campus claiming they have support from another group of students.
"The students arranged a bed sheet and turned it into a screen to see my film. Many watched it and realised it's not what they were thinking. It is a realistic film," Agnihotri, the director of "Hate Story" and "Goal" told PTI.