Anticipating untoward incidents, the administration had deployed security guards in front of all the schools and centres and advised them to videograph "unruly" incidents.
The circular issued by Registrar Pramod Kumar for the deployment of security guards was also burnt by the students.
"In a shocking move, the JNU administration, in order to intimidate the students, had deployed guards at all the school buildings in response to the strike," the JNUSU said in a statement and condemned the administration for treating the students as "criminals".
The JNUSU, along with the JNU Teachers' Union (JNUTA), had announced that it would defy the direction.
The JNUTA had said it was "unproductive" and would lead to the teachers doing a "meaningless" form of bureaucratic work.