A bench of justices Aftab Alam and Ranjana Prakash Desai limited the number of seats to be allocated under the discretionary quota by the President to 100, Vice President to 75, Prime Minister to 75 and the External Affairs Minister to 50.
The bench said 200 seats would be reserved for the Haj Committee of India (HCI).
The court was informed that 11,000 seats have been reserved under government quota to be allocated for Haj 2012.
After limiting the seats under dignitaries quota and the HCI, the bench said remaining seats would go to the Haj committees of various states and Union territories.
It also said no high court will entertain any writ petition for registration of pilgrims for the Haj 2012.
The bench said if any such petition by any pilgrim or private tour operator is filed in any high court, it will have to be transferred to the apex court.
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The bench passed the order after going through an affidavit filed by the government in compliance with the court's May 8 direction.
The court on May 8 had asked the government to furnish details on how its discretionary quota seats for Haj pilgrims are allocated to applicants on recommendation by dignitaries and eminent persons.
It had passed the order saying "we have some initial reservations on allocation of seats on recommendation by dignitaries and eminent persons".
The apex court had also directed the government to phase out Haj subsidy within a period of 10 years, saying the sum can be more profitably used for social and educational development of the Muslim community.