The complaint was filed with the university's Gender Sensitisation Committee against Sexual Harassment (GSCASH) against JNUSU President Akbar Chawdhary and joint secretary Sarfaraz Hamid on July 24.
The issue came to light yesterday after posters came up in university premises through which the two student leaders denied charges of sexual harassment.
"We would like to inform the student community that a complaint in GSCASH has been filed against us. We were informed of this complaint on July 24 and were shocked by it," a joint statement released by Chawdhary and Hamid said.
"If the GSCASH takes up the complaint for enquiry, we will step down from our posts in the JNUSU and our organisation and cooperate fully with the enquiry," it said.
In keeping with those rules, procedures and principles that we all hold dear, we are bound to engage in public discussion regarding the complaint or put forward a public defence in any way," the statement said.
Meanwhile, members of the GSCASH have remain tight-lipped about the issue.
However, a GSCASH member said a committee would be set up to look into the case.
"There will be a complaint screening committee meeting this week and subsequently, probe will be taken further," the member said.