After Speaker Kavinder Gupta allowed an adjournment motion moved by the opposition, the National Conference leader said there had also been unrest in the valley in 2008 and 2010 but "we did not blame the opposition" for that.
"The situation in 2010 cannot be compared with that of 2016," he told the assembly.
"We did not blame Pakistan or the opposition for the situation. I did not blame my officials in 2010.
"In 2016, the media was attacked and newspaper offices were raided.
"We made mistakes and I accepted making mistakes while handling the situation."
Taking a dig at Mehbooba, Omar Abdullah said: "You blamed Jawaharlal Nehru, my father, my grandfather and police for militancy in the state.
"Did you ever blame yourself for your failure to restore normalcy in Kashmir?"
Omar Abdullah said the state government had completely failed in dealing with the situation after the killing of militant Burhan Wani on July 8 last year.
Instead of blaming the opposition, the Chief Minister should accept the responsibility for the failure of her administration and the killings of nearly 100 civilians during the unrest, he said.
Meanwhile, Bharatiya Janata Party MLAs continued to seek an apology from the National Conference and the Congress for allegedly disrespecting the national anthem on Monday during the joint session of the assembly.
Earlier, the opposition disrupted proceedings in both the assembly and the council seeking discussion on the valley's unrest.
The Speaker had allowed the discussion after the treasury benches said they had no objection to discussing the unrest.