A bench headed by Chief Justice J S Khehar questioned the state government over granting Rs 100 crore to educational bodies, allegedly without following procedures.
"How could the money be allocated to a society without any guarantee of returns and scrutiny? ...The state government should clarify its stand," the bench, also comprising Justice D Y Chandrachud, said.
The top court asked UP's Yogi Adityanath government to file a response on the issue within two weeks.
The auditor in a report had said an amount of Rs 35 crore was irregularly given to the Chaudhury Charan Singh College in Etawah.
The court was told by CAG that proper procedures were not followed in releasing contingency funds to a college by the UP Rajkiya Nirman Nigam Limited, a subsidiary of the PWD department, and "gross irregularities" were found in the disbursal of funds.
The apex court had earlier asked the Centre to inform it if CAG had objected to the release of funds in connection with the birth centenary celebrations of former Prime Minister Charan Singh to the college run by a society which had senior Samajwadi Party (SP) leaders on its Board.
The bench is hearing an appeal filed by one Mahendra Nath Rai against the dismissal of his plea in 2004 by the Lucknow bench of the Allahabad High Court, challenging the grant to the college for the centenary celebration in 2002-03.
The court had also asked Siksha Prasar Samiti, the society which runs the college, to inform it within four weeks about its composition and income tax returns, giving details of the inflow of funds.
The court had on March 2 expressed displeasure over the non-filing of responses by some people, including the ex-chief minister, in the case for which notices were issued in 2005.
The plea alleged that the centenary celebrations had taken the form of construction of buildings for the college being run by the society and the expenditure incurred by the state was released through the UP Rajkiya Nirman Nigam Limited.
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