"Hum kya chahe - Azadi. Kashmir ki Azadi. Manipur ki Azadi. Nagaland ki Azadi (We demand freedom. Kashmir's freedom. Manipur's freedom. Nagaland's freedom)," one of the posters said.
All such posters were signed by a group called 'RADICAL'.
Both the student unions and authorities have distanced themselves from such posters.
"These are some fringe elements. I met the students union leaders in the morning and they told me that they disassociate themselves with all anti-national slogans," Vice Chancellor Suranjan Das said.
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"As a Vice Chancellor, it is my responsibility to see that the students get their right to protest, their freedom of speech and expression is protected," he said.
On whether the university would make any police complaint on this issue, he said the question did not arise.
Sounak Mukherjee, leader of Forum of Art Students--a students union--said the majority view of the students was not reflected in the posters.
"We are against it," he said.
In the meantime, two opposing groups of students brought out rallies in the campus.
The smaller group shouted slogans of 'Bharat Mata ki Jai' and voiced their concerns against yesterday's torch rally.
They shouted slogans against eulogising Afzal.
As a counter to this, other students also brought out a rally.
The SFI state unit distanced itself from the pro-Afzal Guru slogans, saying they do not support it and the entire student community of JU should not be blamed for such "irresponsible slogans".
SFI(CPI-M's student wing), AISF (CPI student wing) along
with other Left students unions took out a rally today from College Square to Esplanade in Kolkata to express solidarity with their JNU counterparts who are agitating against the arrest of their leader Kanhaiya Kumar for alleged sedition.
Das in a statement said "Presently there is a tendency to polarize the nation on the basis of radical nationalism and attempts are being made to malign the Left parties. In such a scenario such irresponsible statements will only strengthen the fascist forces and weaken the student's movement."
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The JU vice-chancellor said he would act according to university procedures if he receives a complaint.
Later in the evening a small group of students carrying the national flag brought down many of the posters.
The students did not identify themselves as belonging to any union or political ideology and said "We will clean away all anti-national posters".
Meanwhile, no complaint has yet been registered at Jadavpur police station on JU rally yesterday.
"We are looking into the matter extensively and if there is any violation then legal steps will be taken against the accused," Joint CP (HQ) Supratim Sarkar said.
"The agitation was anti-national. It was done at the behest of the Communist parties. They are supporting terrorists like Afzal Guru," he added.