Mookerjee went to visit Kashmir in 1953, and went on hunger strike to protest the law prohibiting Indian citizens from settling in a state in their own country and the need to carry ID cards, and was arrested on 11th May while crossing border. Although the ID card rule was revoked owing to his efforts, he died as detenu on May 23, 1953 under mysterious circumstances. His death in custody raised wide suspicion across the country and demands for independent enquiry, including earnest requests from his mother, Jogmaya Devi to the then Prime Minister of India, Jawaharlal Nehru. Unfortunately no enquiry commission was set up and his death remains a mystery.