"When one questions the very existence and integrity of the republic, then it goes beyond dissent," he said while attending a private function here.
Dissent is the "essence of democracy", but when it crosses limits and comes to challenge the unity and integrity of the nation, it does not remain so, the Minister of State in the Prime Minister's Office said.
He said the impression being projected by some parties that students are being harassed is misplaced.
Asked about the remarks of Rajnath Singh linking the JNU incident with Lashkar-e-Taiba founder Hafiz Saeed, the minister said everything has become clear after the Union Home Minister spoke on the issue.
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"The incident at JNU received support from Hafiz Saeed. This is a truth that the nation needs to understand," Rajnath had said on Sunday.
The matter kicked off a political slugfest as BJP termed it "treason" while Congress and the Left have termed the police action as being "unacceptable" and likened it to the "situation during Emergency".