Sen, who confirmed his resignation when contacted, had taken over from Dhrubojyoti Chatterjee in 2015 and was from the commerce faculty. His tenure in office was till 2019.
Chatterjee told a press conference that Sen, had not told him about the move before taking the step.
"How can I say why he took such a step? I can't also comment on why he has quit before the end of his term. If someone wants to return to teaching assignments it is not bad," he said to a question.