Claiming the charges against Jawaharlal Nehru University (JNU) students were "baseless", he said BJP's "hidden agenda" is to "saffronise the educational system and atmosphere".
"The same attitude is being adopted in case of Jamia Millia Islamia and Aligarh Muslim University," he said.
"The students cannot raise voice against their own country and Constitution. It is BJP's inclination to close down JNU," the minister said.
He said the action against the students was part of BJP's "strategy to depute its own agents who opted slogan-mongering".
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Khan said had BJP not received the electoral drubbing in Bihar "some very dangerous events might have emerged".
In a veiled attack on Prime Minister Narendra Modi over his stopover in Pakistan, the minister said, "PM had arranged a trip to Pakistan on the advice of a capitalist without taking Parliament into confidence and overlooked the consequences of visiting such a country where even a nine-year-old boy walks with rocket launcher."