The protest took place after Dr Khan's nephew Shaikh Usman accused him of committing blasphemy by writing objectionable comments on Islam in his book, reports the Daily Times.
Usman has reportedly made repeated visits to 19 police stations seeking to lodge an FIR against his uncle. The police, however, refused to register any case without investigating the allegation.
Police said the protesting clerics had pointed to certain references in the notes of Dr Khan that included discussion on Islam and the Prophet Mohammad, but added that it was difficult to say if the material constituted blasphemy as defined by the law.
Police said it has sent the same to legal branch to establish the charge.
Dr Khan is said to be a PhD scholar who has authored several books on different topics.