Terming as baseless the case against Advani, he said the BJP patriarch had expressed deep regret at Babri mosque demolition and even called it the saddest day of his life.
Had the apex court given a direction for day to day hearing earlier, the guilty would have been punished and the name of innocents cleared by now, Kulkarni said.
"For the Supreme Court to revive the criminal conspiracy case after 25 long years raises a very serious question mark on functioning of India's judiciary," Kulkarni told PTI.
"Had the apex court given a direction, say 20 years ago, for a day to day hearing, and quick appeal and disposal at higher courts, the case would have ended long ago, the guilty punished and the name of innocents cleared," Kulkarni, chairman of the Mumbai-based think tank Observer Research Foundation, said.
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"The case of criminal conspiracy against Advani is baseless. He was not a part of the conspiracy at all. In fact, he expressed deep regret at what happened and wrote soon after the Babri demolition that it was the saddest day of his life," Kulkarni said.
"I am certain that Advani ji will come out innocent in this case," he said.
"The Babri demolition was condemnable. It seriously affected communal peace in India. However, even at this stage, all efforts should be made by leaders of the two communities to arrive at an amicable settlement which respects the sentiments of both Hindus and Muslims," Kulkarni said.
Asked if the delay in the court verdict would mar the veteran BJP leader's chances of being in the race for the President's post, Kulkarni said, "I wouldn't like to comment on this.