During the meeting, the ruling and opposition parties assured their cooperation for a productive Winter Session of Rajya Sabha that starts Tuesday and sought equitable allocation of time.
Around 31 leaders, including ministers, attended the meeting convened by Naidu.
The Rajya Sabha would be adjourned for the day on the first day after obituary references for former prime minister Atal Bihari Vajpayee.
While both the ruling and opposition parties assured the chairman of their full cooperation for a productive session, Leader of the House Arun Jaitley and Leader of the Opposition in Rajya Sabha Gulam Nabi Azad spoke of their keenness on a "meaningful and productive" session.
Both of them sought equitable allocation of time for the government's legislative proposals and the issues that opposition seeks to raise in the House.
In his opening remarks, Naidu urged the leaders of all sides in the House to ensure a productive Winter Session which would be the last full-fledged one before the general elections next year.
Naidu called upon them to "aid, assist and advise" him in ensuring a smooth session. He noted that both the government and the opposition have the right to pursue respective agendas but that should be done while ensuring effective functioning of the House.
The chairman hailed the high voter turnout in the Assembly polls in five states as yet another indication of the people's faith in parliamentary democracy and a reminder that legislatures need to rise to their expectations.
He complimented the Election Commission, the state governments and the people for the successful conduct of polls.
He informed the leaders that to further the success of e-notice (submission of notices by members online) during last session, it has now been decided that notices of members for submission of Zero Hour notices will now be accepted up to 9.30 am instead of the earlier 10 am on each sitting of the House.
He said this advancement would give him more time to properly prioritise such notices in the available time.
Jaitely said the government was willing to discuss any issue if time was properly allocated for both the government and the opposition, while Azad said the opposition wanted the House to function and bills to be passed.