Bolpur Sub-divisional Police Officer Suryaprasad Yadav said the three were arrested from the university campus.
The fourth accused, however, was yet to be arrested.
Earlier in the day, Visva-Bharati Proctor, Prof Harish Chandra Mishra lodged a complaint with the police against four persons, including three students of Kala Bhavan (school of fine arts).
The university also suspended the three accused students pending further investigation, a spokesman of the central varsity said.
The SDPO said the police initiated investigation after receiving the compliant against three students and 'an unknown outsider' against whom the Sikkimese girl, a second year student of Kala Bhavan, levelled her allegation.
The girl first lodged a complaint to the departmental head on Tuesday and then to the Vice-Chancellor Susanta Datta Gupta on Thursday.
She alleged in her complaint that the accused 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.
The girl's father met the Vice-Chancellor yesterday and demanded steps against the culprits.
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.