A bench headed by Justice K S Radhakrishnan asked the government to file a proper application seeking modification of its earlier order in which it had refused to stay the High Court order.
Solicitor General Mohan Prasaran submitted that in a similar case the apex court had permitted the Andhra Pradesh government to implement reservation for backward Muslims within the state till the matter is decided by it.
The petitioner, on whose plea the High Court had quashed Centre's decision, opposed the Centre's plea, saying that it is politically motivated with an eye on elections.
The bench, however, said that it will look into the issue.
The apex court in June, 2012 had refused to stay the High Court order that quashed 4.5 per cent sub-quota and had ticked off the government for the way it had handled the "complex and sensitive issue".
On May 28, 2012, the Andhra Pradesh High Court had struck down the government's sub-quota for minorities, and had held that the Centre acted in a "casual manner".
It had said that the government Office Memorandum (OM) creating the sub-quota was based on religious grounds and not on any other intelligible consideration.
"No evidence has been shown to us by the learned Assistant Solicitor General to justify the classification of these religious minorities as a homogeneous group or as more backward classes deserving some special treatment. We must therefore, hold that Muslims, Christians, Sikhs, Buddhists and Zoroastrians (Parsis) do not form a homogeneous group but a heterogeneous group," the bench had observed.
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