Visva-Bharati Proctor, Prof Harish Chandra Mishra, lodged the complaint with the police against four persons, including three students of Kala Bhavan (school of fine arts).
The Visva-Bharati also suspended the three accused students pending further investigation, a spokesman of the central university said.
Bolpur Sub-divisional Police Officer Suryaprasad Yadav said the university lodged the complaint against three students and "an unknown outsider".
"We have initiated investigation after receiving the compliant," the SDPO said.
The "unknown outsider" was among those against whom the Sikkimese girl, a second year student of Kala Bhavan, levelled her allegation.
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She alleged in her complaint that they had sexually harassed her and clicked some photographs with their mobile phones and threatened her to blackmail with those.
As soon as the complaint was brought to the vice-chancellor, he asked Mousumi Bhattacharya, Chairperson of the Internal Complaint Committee for Prevention of Sexual Harassment Against Women at Workplace, to investigate, said Vice-Chancellor's spokesperson Prof Sandip Basu Sarbadhikary.
"The committee has given its report within 48 hours. Based on that an FIR has been lodged. The Visva-Bharati has suspended the three accused students of Kala Bhavan pending further investigation," the statement said.
After the meeting, the girl and her father were taken to Bolpur railway station in a university car from where they left for Kolkata by the Saraighat Express.