He also criticised the organisers of the meeting to commemorate the death anniversary of Guru on JNU campus, which set off a chain reaction of protests and counter-protests.
"Whether the leaders who are visiting JNU are giving moral support to Afzal Guru's supporters and (for) dividing India. They are poisoning the varsities," the Urban Development Minister said after laying the foundation stone of Society for Applied Microwave Electronics Engineering and Research (SAMEER) here.
"What a great shame and a stupid idea to organise such a meeting. Afzal Guru was the co-conspirator of the attack on Parliament which was the attack on our democracy. Our brave security forces sacrificed their lives to protect 740 people's representatives.
"We are not saying that the entire university (JNU) is like that, but there are such elements that are to be isolated, separated and toughly acted on," Naidu said.
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He said tough action should be taken against those "elements" who raise "anti-national" slogans.
On allegation of "rising intolerance" in the country, Naidu said, "They (raising the allegation) should take note that India is known for its utmost tolerance in entire world".
Referring to the JNU row, he said no country compromises on its sovereignty, integrity and unity.