The hoarding had been put up by the Trinamool Congress -affiliated teaching and non-teaching staff wing of the university thanking the chief minister for announcing Rs 100 crore grant for JU recently.
There were scribbles in black ink mocking the message in the hoarding that was discovered on Sunday.
Vice Chancellor Prof Suranjan Das said, the defacement was very unfortunate and the Executive Council has already taken up the issue with the students and faculty.
"We have already discussed the issue at the EC meeting and we will ensure such things do not recur in future," the VC said.
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Das was confined in the administrative building of the university, along with other EC members due to a sit-in by students over the alleged attempt to dissolve students' union, since last afternoon.
Das said, in a democracy, everyone has the right to put up posters and hoardings in a public place.
An Arts Faculty Students' Union spokesperson said the union did not support any such act and claimed that it did not have any knowledge about the involvement of any member.