The students sat outside his office shouting slogans demanding his resignation, stopping short of a gherao this time.
"The VC today came to the campus around 12 noon and went to his office. We have decided to continue with the academic strike unless he resigns, but we won't gherao him," said Gitoshree, a member of JU students' union.
West Bengal Governor K N Tripathi, who is the Chancellor of the university, said "outsiders" had fomented trouble inside the prestigious institution.
"Let the university not be politicised... Let it be a centre of excellent education," he added.
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Asked if he has received any letter from R Chidambaram, chairman of the three-member search committee constituted by the state government, to suggest names for the post of JU Vice-Chancellor, Tripathi said, "I've not received any letter from anybody."
Thousands of students had marched through the city's streets last Saturday demanding Chakraborty's resignation.
Meanwhile, students in the JU mass communication department had boycotted their examination on September 18.