During a debate on Kashmir situation, Ganai said Burhan was a "martyr" and that he had "given up his life for the cause of Jammu and Kashmir".
His remark drew protests from BJP and PDP members.
PDP member Firdos Tak said such words should not be spoken on the floor of House.
However, Ganai stood by his remarks and added, "Kashmir is political problem and youth have taken to guns."
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Burhan, commander of Hizbul Mujahideen terror outfit, was killed in an encounter with the security forces in a village of Anantnag district in Kashmir on July 8 last year.
Later, speaking to reporters outside the Council, Ganai said "Burhan Wani is a martyr.
He claimed that there was no FIR or a case against Burhan till 2015 when BJP and PDP government came, and it is they who had said that there was no case of militancy registered against him.
"I don't know how you can brand him as a terrorist. Jammu and Kashmir is an issue and if he has raised this issue and given sacrifice of his life, he is a martyr. It is my personal opinion, not that of the party," the NC MLC said.
"Government of India slowly and steadily eroded the special position of Jammu and Kashmir. If some people fight for restoration of that special status and he loses his life in the fight, what can be he called, he is a martyr?"
Reacting to NC MLC's remarks, Leader of the House and Education Minister Naeem Akhtar said, "It has become a fashion to say that those killed in Kashmir are our children. They are not our children. They (some politicians) do politics on them and nothing else. We did nothing to save them. They are further pushing them into it. They should be asked what they saying."
Slamming the remarks, Ambardar said, "it is very unfortunate. NC is a very responsible party and their legislator talks of a separatist language".
The BJP MLC recalled that Pakistan Prime Minister Nawaz Sharif, during his address to the UN General Assembly in September last, had also described Burhan as a "Kashmiri leader".
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In the Legislative Council, PDP lawmaker Firdous Tak interrupted Ganai and sought clarification from him to confirm whether his remarks represented his party or were his personal opinion.
Tak said, "the statement of member just made in the House is very sensitive; this message would go outside, so he must know what he is speaking in the House."
Reacting to this, Ganai said, "I am fully aware about the place where I made the statement and I stand by each word I have said about Burhan Wani.