The former Supreme Court judge gave his resignation to Governor M K Narayanan when he met him at Raj Bhavan, the sources said.
Justice Ganguly was with the governor for about 45 minutes.
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When asked whether he had resigned, Ganguly replied “I won’t comment.”
“It is a good thing that he has resigned a day after talking to me,” former Attorney-General Soli Sorabjee said in Delhi.
Ganguly had telephoned him on Sunday and said he was contemplating resigning as WBHRC chairman.
Additional Solicitor General Indira Jaising, who has been strongly pitching for his removal as the human rights panel chief, said it was “overdue”. The senior advocate said it was a “right decision”.