Prime Minister Narendra Modi, who also attended the meeting, made a brief intervention hoping that the three-month long session, beginning February 23, would be a "very constructive and positive" affair.
However, there was enough indication that the crucial bills like GST are unlikely to be taken up in the first half of the session, which concludes on March 16.
There is a view in BJP that a debate on the JNU row will revolve around the issue of nationalism which will work to its advantage.
In the meeting, the Opposition and the government also agreed to pass a bill without discussion in RS on delimitation exercise in West Bengal to grant voting rights to people who came to India from Bangladeshi enclaves.
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Finance Minister Arun Jaitley, who spoke first in the meeting, sought the Opposition cooperation for the same, to which West Bengal's ruling Trinamool Congress agreed.
Immediately after the meeting called by Ansari, Opposition leaders huddled together to chalk out a common floor strategy.
A meeting of the Congress Working Committee has been convened by party chief Sonia Gandhi on the eve of the session.
At the all party meeting, D Raja (CPI) urged Ansari to hold a structured discussion on the JNU issue and take it up on a priority basis while K C Tyagi from JD(U) accused the government of "targetting" Opposition parties, and speaking the language of Congress during the Emergency.
Azad said that a number of incidents have happened in
recent times, which are "agitating" the minds of people like the incident in JNU, bashing up of journalists in court premises and a dalit scholar's suicide in Hyderabad.
"All these issues need to be discussed threadbare," he insisted.
Asked whether the pending bills on GST and real estate could also be taken up, Azad said these were not discussed.
Another party leader indicated that these bills could only be taken up in the second half of the budget session, which begins from April 25 and ends on May 13.
Azad said that Opposition also wants to discuss issues like price rise and farmers' suicide.
Tyagi said that while the Opposition wants Parliament to run, "the unilaterism of the ruling party will not be allowed".
The meeting was also attended by Rajya Sabha Deputy Chairman P J Kurien, Deputy Leader of Congress in Rajya Sabha Anand Sharma besides representatives of JD(U), CPI, CPI(M), RJD, SAD and NCP.
He added that the first part of the budget session should be devoted towards passing urgent bills besides the budget.
"The meeting ended with a general sense of agreement that the House should legislate and deliberate on all issues. All leaders present shared the same feeling. The Prime Minister held that it has been a good meeting and hoped that the session will work," a communique from the Rajya Sabha said.
Apparently concerned over the virtual wash out of last two sessions, Ansari called the meeting amid the possibility of a tumultuous session.
Rajya Sabha, where the government lacks majority, had seen repeated disruption in the monsoon and winter sessions with Congress and several other opposition parties blocking key economic reform measures of the Modi government.
Lok Sabha Speaker Sumitra Mahajan and Parliamentary Affairs Minister M Venkaiah Naidu have also called separate all-party meetings on February 22, a day before the session begins.
The government is keen to push its legislative agenda in the budget session, including the pending bills on GST and real estate that were thwarted in the last two sessions.