Mehbooba also indicated that had the security forces known about Wani's presence the situation could have perhaps been controlled better.
She said had the security forces known about Wani being present inside the house in Kokernag area of South Kashmir's Anantnag district, it would have been possible to keep the situation "from turning to what it is today."
"I feel if they knew, perhaps we would not have such a situation when the overall situation in the state was improving, so it could have been a chance," she told reporters.
The statement from the chief minister came immediately after opposition National Conference Provincial President Nasir Wani said the chief minister was aware of the operation and had also rewarded the officials who led the operation in which 22-year-old Wani was killed on July 8.
"How can one know everything about every encounter?"
"As far as I know, what I heard from the police and the army, who said they only knew that there were three militants inside the house but did not know who they were," she told reporters.
The statement comes nearly three weeks after Wani along with two others were killed at Kokernag in South Kashmir.
Additional Director General of Police S M Sahai had told reporters after the operation that the chief minister was aware about the operation.
The police and intelligence agencies are saying that they did not know who was there, Mehbooba said.
The chief minister said the government did not get enough time to make arrangements to contain the situation, unlike when Parliament attack convict Afzal Guru was hanged in 2013.
"When Afzal Guru was hanged, (then chief minister) Omar (Abdullah) knew, so he made all the arrangements beforehand. We knew nothing and we came to know suddenly. But, despite that, we tried to impose curfew so that children do not come out," she said.
Violence has rocked the Valley since July 8, when Wani was killed in an encounter, leaving 47 people dead. At least 5,500 people, including 3,000 security personnel, have also been injured.
Mehbooba said an atmosphere should be created in the state for peace and dialogue and the government would do "everything" to provide relief to the people affected by the violence.
"An atmosphere should be created in Jammu and Kashmir where there is dialogue, transparency like in (former Prime Minister Atal Behari) Vajpayee's time when a peace process was started and there was ceasefire with Pakistan," Mehbooba said.
Image: Jammu and Kashmir Chief Minister Mehbooba Mufti addresses a press conference. Photograph: Umar Ganie/Rediff.com