Modi was chief minister of the western state during the violence that killed more than 2,000 people, most of them Muslims.
The students' union of New Delhi's Jawaharlal Nehru University, long seen as a bastion of left-wing politics, said on Twitter it would screen the documentary, 'India: The Modi Question', at a cafeteria at 9:00pm (1530 GMT).
On its website, the university administration said it had not given permission for the showing.
"This is to emphasise that such an unauthorised activity may disturb peace and harmony of the university campus," it added.
"The concerned students/individuals are firmly advised to cancel the proposed programme immediately, failing which a strict disciplinary action may be initiated as per the university rules."
On Twitter, the union president, Aishe Ghosh, had asked students to attend the screening of the documentary, describing it as having been "'banned' by an 'elected government' of the largest 'democracy'".
Asked by Reuters if the union planned to go ahead with the screening, Ghosh responded, "Yes, we are."
She declined to comment on the university's threat of disciplinary action, however.
Police are closely watching the situation, said a Delhi police officer monitoring the area around JNU. But police in the capital declined to make any official comment.
The documentary is also set to be screened at some campuses in the Communist-ruled southern state of Kerala.
India's home ministry did not immediately respond to requests for comment on the government's plans if the film is shown at JNU and in Kerala.
The 2002 Gujarat violence erupted after a train carrying Hindu pilgrims caught fire, killing 59. Crowds later rampaged through Muslim neighbourhoods. In 2017, 11 men were jailed for life for setting the train ablaze.
Modi has denied accusations that he did not do enough to stop the riots and was exonerated in 2012 following an inquiry overseen by the Supreme Court. Another petition questioning his exoneration was dismissed last year.
Last week, the BBC said the documentary was "rigorously researched" and involved a "wide range" of voices and opinions, including responses from people in Modi's Hindu nationalist Bharatiya Janata Party.