In a statement, the union's vice president Anubhuti Agnes Bara and general secretary Sandeep Saurav said JNUSU President Akbar Chawdhary and Joint Secretary Sarfaraz Hamid were no longer holding their offices.
"The President and the Joint Secretary have resigned. As per the constitution, JNUSU vice-president will now look after the work of the president also," said Saurav.
A member of the university's Gender Sensitisation Committee against Sexual Harassment (GSCASH) said the committee did not demand their resignation against whom a complaint of sexual harassment was filed.
The resignations come days after Chawdhary and Hamid had announced through posters that a case of sexual harassment has been filed against them with the GSCASH.
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"We would like to inform the student community that a complaint with GSCASH has been filed against us. We were informed of this complaint on July 24 and were shocked," said a joint statement released by Chawdhary and Hamid on July 28.
They were criticized by the committee for going public with the complaint.
As per GSCASH rules, once a complaint is filed with the office, a restraint order is given to each defendant.
"According to the restraint order, which is signed individually by each defendant, there cannot be any public declaration regarding the case. The defendants are not allowed to issue a public notice stating that a case has been filed against them," the GSCASH had said in a statement.