A complaint was filed on Friday against the teacher who is a faculty member at the university's School of Social Sciences.
"A student of JNU has complained against a professor at the Vasant Kunj Police Station that he misbehaved with her two days back. An FIR under Section 354 of the Indian Penal Code for sexual harassment has been lodged. We are investigating the matter," a senior police officer told IANS.
The university administration, however, said it had not received any complaints of molestation from any student.
"We don't know of the particulars of the case. Unless a student files a complaint with the Internal Complaints Committee of the university, we cannot take any action," JNU Registrar Pramod Kumar told IANS.
This is the third case of molestation in the university in recent months. Four professors in two different cases were accused of harassment earlier.
A police complaint was filed only in one case, while in the other case where three professors were accused of harassment, a complaint was raised internally.