A bench, comprising justices J S Khehar and C Nagappan, also pulled up the counsel for Maharashtra for opposing the bail plea of Saibaba.
"You have been extremely unfair to the accused, especially looking at his medical condition. If material witnesses have been examined, then there is no point in putting him in jail," the bench said.
Counsel for Maharashtra government said some crucial prosecution witnesses need to be examined.
On February 29, the apex court bench comprising justices J S Khehar and C Nagappan had said it may consider granting bail to Saibaba after the trial court examined key witnesses, and had directed day-to-day hearing in the case.
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Earlier, the court had asked the Maharashtra government to look for an alternative arrangement to house the jailed professor.
Prior to this, the apex court, on a plea of author Arundhati Roy, had refused to stay a criminal contempt notice issued by Bombay High Court against her for an article in a weekly magazine questioning the continued incarceration of Saibaba.
The Bombay High Court had on December 23, 2015 issued the contempt notice against the author for her views on Saibaba's arrest and rejection of his bail plea early last year.
Gadchiroli Police had arrested Saibaba in 2014 for his alleged links with Maoists. He has been on bail since June last year.