He also expressed concern over the "negative public perception" that was being created by these disruptions which were adversely impacting the image and credibility of the House.
Naidu's remarks came after the Rajya Sabha was adjourned twice till late afternoon today due to protests by opposition members including those from the Congress and the Trinamool Congress, who alleged that their voice was being "muzzled".
Naidu said he was committed to allow all members to raise any issue as per rules and procedures and "none should have any misgiving about that."
Apparently pointing to the opposition leaders, he said some members have not properly understood his concern and anguish over the functioning of the House.
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"I realise some members have perhaps not properly understood my concern and anguish over the functioning of the House. I would like to reiterate again that it would be my commitment to allow any issue to be raised by anybody as per rules and procedures and nobody should have any misgivings about that," he said.
Noting that the disruptions "frequently follow a pattern", he said it was aimed at not allowing the House to function smoothly, come what may.
Elaborating on the pattern of disruptions, Naidu said he has admitted a total of 42 zero hour admissions during the last three working days and observed that of these, only one member could make a submission.
"Another aspect of this pattern is that first zero hour is disrupted and then even question hour when the members get an opportunity to question the government, that is also disrupted," he said.
"In this era of TV explosion, such frequent adjournments are adversely impacting the image and credibility of this house," Naidu said.
"In this backdrop, I thought it would be better to adjourn the House for a longer period instead of resorting to frequent adjournments. That too, when it becomes evident that some sections of the House were bent on not allowing smooth conduct of the House," he said.
Naidu said he discussed this concern with Deputy Chairman P J Kurien earlier in the day and later with the floor leaders of parties and urged them to ensure smooth conduct of the proceedings.
Naidu poured out his anguish hours after opposition members led by Leader of Opposition Ghulam Nabi Azad and Derek O'Brien of TMC protested over the long adjournments.
They also did not agree to Dy Speaker Kurien's suggestion to meet the the Chairman in his chamber and resolve the deadlock. "I would request you to be in he Chairman's Chamber. I cannot resolve (the issue) here," said Kurien.
But, O'Brien pressed for an open debate in the House, saying "Whatever has happened at 11.10 AM did not happen in the chamber, but here only."
"Let every one speak for one minute only," he said, adding "our voice is muzzled outside and even inside."
Several other opposition members were also on their feet, demanding debate over a notice moved under rule 267 that was earlier rejected by the Chair.