Mamata Banerjee had called Mr Chowdhury a Maoist after he asked her a question on the rising fertiliser prices at a public rally on August 8 last year in West Midnapore district.
Angry at the question, Ms Banerjee had asked the police to arrest Mr Chowdhury on August 10, two days after the incident.
Accused of allegedly grievously hurting policemen on duty at the rally, Mr Chowdhury had to spend 14 days in jail and still has two cases filed against him.
"It is now proved that I was innocent. I urge the government to heed the human rights commission andprotect democracy," Mr Chowdhury told NDTV today.
Professor Mahapatra has not received the compensation yet.