The Commission directed the government to maintain the status quo in the matter as ordered by the High Court of Meghalaya twice earlier and furnish a detailed report.
Former IPS officer Iqbal Singh Lalpura said that minorities are '100 per cent secure' under Prime Minister Narendra Modi's government.
The order was passed after the Centre made a plea to extend the deadline by a period of three months.
The submission was made in an affidavit filed in response to a petition which said welfare schemes cannot be based on religion.
The former Uttar Pradesh Shia Central Waqf Board chairman had moved the Supreme Court with a plea seeking the removal of certain verses from the Quran claiming they promote violence.