Justice Manmohan referred the matter to a Division Bench headed by Chief Justice G Rohini which is likely to hear it on May 28.
Earlier, the Supreme Court had refused to interfere with the government's decision.
Navalokam Samskarika Kendram of Kottayam, Kerala, in its plea has alleged that the Ministry of Sports and Youth Affairs not only selected the athlete but also sent the prize money of Rs five lakh through cheque, besides the air ticket.
The ministry decided not to confer the award as the triple jumper was found to have used a 'scheduled' substance (ephedrine) back in 2008.
Besides the Ministry, the plea has also made Sports Authority of India, Athletic Federation of India and Director General of National Anti Doping Agency as parties.
The petition has sought quashing of the alleged 2008 dope test report of the athlete on the ground that the National Anti-Doping Agency has not been accredited by the World Anti-Doping Agency and the "custody of the sample" did not satisfy the legal requirements.
His name was in the award list released on August 14, 2013. On August 29, he came to Delhi from Chennai and stayed at Hotel Ashoka, along with other award winners, and participated in a rehearsal at Rashtrapati Bhavan for the function, the plea said.
The next morning, he was told to stay away from the ceremony as the award had been withdrawn, it said.
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