The activists, under the banner of 'Bharat Bachao Sangathan', staged a silent protest outside Bhabani Bhavan with banners reading 'Jurisprudence calls for arrest of Mr Ashok Ganguly'.
They also submitted a letter to his office, saying that since he has been accused in the case and a three-member committee is looking into it, Ganguly should resign from the post to ensure a free and fair trial.
They also submitted a letter to governor M K Narayanan, requesting him to ask Ganguly to step down from the post.
Denying allegations of the intern, Ganguly has so far declined to say whether he would resign as WBHRC chief.
Trinamool Congress leaders had also demanded that Ganguly should step down from the post.