A bench of Justice B D Ahmed and Justice Siddharth Mridul also sought a status report from the government's Directorate of Education (DoE) saying it should spell out the steps taken on the issue.
"What DoE is doing. It is doing nothing. Please let us know what is the status," the bench said, while seeking the report within eight weeks.
The court has fixed the matter for further hearing on October 28.
The direction came after the bench was informed that the unaided schools have failed to refund the excess fees as per its earlier order.
The court had also said that the committee has submitted four reports based on examination of fee structures of unaided private schools and questioned why the government has not initiated the process of refunding the excess fee.
The Justice Anil Dev Singh Committee, which had made the recommendations, has so far examined the accounts of around 605 unaided private schools out of a total 1,172 institutions.
After the implementation of the Sixth Pay Commission report, the schools increased the fees, citing additional financial burden due to increased salaries of teachers.
In August 2011, the court gave directions for setting up a three-member committee to audit the accounts of each of the schools to ascertain if the fee hike was required.
This order had come on a petition filed by an NGO Social Jurists, through advocate Ashok Agarwal, which had alleged that schools hiked the fees "unreasonably" but failed to pay the salaries of the teaching and non-teaching staff as per the pay panel recommendations.
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