Opposition members trooped into the Well of the House calling the government a "cheat", forcing Deputy Chairman P J Kurien to adjourn the proceedings for about 7 minutes.
The Government vehemently denied the charge, saying if anybody has a problem, they should go to the Election Commission as Parliament is not the forum to agitate.
Congress and SP members gave as many as four notices under rule 267 seeking suspension of business to take up the issue, which the treasury benches vehemently opposed.
Opposition members protested saying the barb was directed at BJP and not to the people, but the protests from treasury benches led Kurien to say he would expunge such remarks from the records.
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Angry exchanges were also witnessed between Naqvi and Leader of the Opposition Ghulam Nabi Azad.
Naqvi said the general elections in 2004 and 2009 and the assembly elections in Bihar, Punjab and Delhi where the BJP lost, were all conducted using EVMs and the Congress did not seem to have any objections then.
When the House met for the day, Digvijaya Singh (Cong) said the testing of EVMs for a by-election in Madhya Pradesh had a few days back had shown manipulations wherein vote would be credited to BJP irrespective of the candidate for whom it has been cast.
He demanded that ballot papers be used for the upcoming by-elections and elections henceforth.
HRD Minister Prakash Javedkar countered him saying the Election Commission has made it clear there can be no manipulation of EVMs and if the opposition had any problem they should go to it and not waste Parliament's time.
BSP, she said, has gone to the court against the use of EVMs. She went on to call it "murder of democracy" and demanded the use of ballot papers in future elections.
Her party's Satish Misra said this was a government of EVMs and the ministers protesting were "EVM ministers." The treasury benches protested these remarks as an insult to the people and democracy.
Kurien said he has not allowed notices under rule 267 but allowed those who had given such notices to make brief submission on the issue. "I am not allowing discussion under 267," he said. "If you want discussion, there are other ways."
Kurien said the Election Commission has clarified that this is not possible.
Leader of the Opposition said free and fair elections are the foundation of Indian democracy but unfortunately for the first time, doubts have been cast over EVMs.
Azad alleged that a "thief" does not rob the entire house but does it only selectively so as not to get caught. And in this case, the EVMs were manipulated in the largest state Uttar Pradesh.
He demanded that by-elections in Madhya Pradesh and the coming assembly polls in Gujarat and Himachal Pradesh be conducted using ballot papers.
"If victory has a glamour, defeat should have grace," he said, a comment which infuriated the opposition who trooped into the Well of the House shouting slogans.
Kurien asked opposition members to take up the issue with the Election Commission.
"This is an issue to be taken up with Election Commission," he said. "Election Commission is to examine if EVM is functioning properly or not. Chair cannot do anything."
As opposition members shouted slogans, he said, "I have to inform you that this is an issue to be taken up with Election Commission not with Chair" before adjourning the proceedings till 1130 hours.