The AMU defended the portrait, saying that Jinnah was a founder of the university and granted life membership of the student union.
It was suspected that the scholar from Tikipora in Lolab area might have joined the Hizbul Mujahideen.
Scores of Banaras Hindu University students also staged a protest at the Lanka Gate in support of the AMU students.
BJP MP Satish Gautam demanded the expulsion of Uttar Pradesh Labour Minister Swami Prasad Maurya from the party for calling Jinnah a 'mahapurush'