"The Congress in a way is in the grip of urban Naxals. That is why its thought has become negative," Modi alleged in his 90-minute speech.
Both Houses met for the first time in the second part of Budget Session and saw repeated adjournments as the Opposition continued protests.
Led by Congress leader Rahul Gandhi, the Opposition members in the Lok Sabha demanded sacking of Union minister Ajay Mishra from the government in connection with the Lakhimpur Kheri violence.
The disruption by Opposition members drew sharp criticism from Prime Minister Modi who accused them of being unable to digest the fact that a large number of new ministers are women, Dalits, tribals and those from other backward classes
The opposition parties were demanding a division of votes as they had moved a motion to send the Bill to a select committee, which was rejected by voice vote.
Proceedings in Rajya Sabha were repeatedly disrupted on Monday before being called off for the day as opposition members protested on the alleged phone-tapping and other issues and demanded discussions on them in the House.
Leader of Opposition Mallikarjun Kharge, speaking on the Motion of Thanks on the President's address, charged the government with not delivering on its various promises, including generating two crore jobs per year.
The party managed only 52 seats on its own and many of its top leadership, including Rahul Gandhi, Mallikarjun Kharge and Jyotiraditya Scindia were defeated in the polls.
The CBI chief's advocate said there was no basis for the Central Vigilance Commission to pass such an order recommending to send him on leave.