The list of 21 students includes JNUSU President Kanhaiya Kumar, Umar Khalid and Anirban Bhattacharya, who were arrested under sedition charges over the event and later released on bail.
During the event anti-national slogans were allegedly raised by the accused as they gathered to mark the death anniversary of Parliament attack convict Afzal Guru.
The circular bearing the names of the students carried a noting by the JNU registrar Pramod Kumar.
Although the university authorities were tight-lipped about the development, the affected students protested the move terming it a violation of the court order.
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He said although the registrations were blocked by the university the online system which generated their registration folio informed they were blocked as they had not paid fines imposed by the administration.
The Joint Secretary of JNUSU, Saurabh Sharma, whose registration has also been blocked, alleged he was punished for acting against "anti-national" elements.
He said the high court had directed for an appellate committee hear the version of the accused students but it has not come out with its report.
An enquiry initiated by the JNU administration had indicted 21 people, including two academics from outside the varsity.
Umar, Anirban, and another student Mujeeb, were rusticated in April, while others were expelled from their hostels or fined.
Police have announced a reward of Rs 50,000 for anyone who can provide information about JNU student Najeeb's whereabouts. A public advertisement has also been issued in this regard, police said.