Proof of the minority status is mandatory for schools and colleges to have a say in reservation quantum and limit interference from the government.

The new rule, introduced by the National Commission for Minority Educational Institutions (NCMEI) on March 1, has been decried as "unconstitutional" by its former chairman.

"All petitioners are required to submit unique ID of the trust/society as given by the Niti Aayog portal NGO Darpan (it is not needed only in cases of institutions run by individuals)," said a commission notification.

It said the unique ID should match corresponding details on the NGO's website.

"While the cases already being heard before the commission will continue to be heard, the minority status certificate will be awarded only after the unique ID is provided by the petitioner," the notification from the commission added.

Justice M.S.A. Siddiqui, a retired judge who served as the commission chairman for a decade from 2004, told The Telegraph the notification was "unconstitutional".

Justice Siddiqui said the notification should be amended immediately. "If a minority institution is not taking any funds from the central or state governments, there is no need to seek any unique ID of the Niti Aayog," he said. The Niti Aayog is the think tank that has replaced the Planning Commission.

Since its inception in 2004, the minority education commission has awarded minority status certificates to nearly 13,000 institutions in the country. However, till now, the commission had not asked any applicant to register with Darpan.

A lawyer from a minority community, who did not wish to be named, said that "this move will discourage minorities to set up institutions. Hardly any minority institution is eyeing government funds. Maybe the government is eyeing their affairs unnecessarily."

Last week, attorney-general Mukul Rohatgi had told the UN Human Rights Council in Geneva that India's religious minorities enjoyed constitutional protection.

Justice Siddiqui cited Article 30 of the Constitution that says "all minorities, whether based on religion or language, shall have the right to establish and administer educational institutions of their choice".

The retired judge added: "This right is subject to certain rules and regulations which must be reasonable and in the interest of academic excellence. But this requirement is neither in the interest of academic excellence nor is it reasonable."

NCMEI member Baltej Singh Mann did not wish to comment. "You contact our secretary. He will give the official version," Mann said. Secretary Madhu Ranjan Kumar could not be reached over the phone or by email.