A bench of Acting Chief Justice Gita Mittal and Justice C Hari Shankar said that it is an important body and the vacant post is "extremely important".
"Please ensure that the appointment is done as soon as possible," the bench said.
The court's direction came during hearing of a PIL filed by Delhi-resident Mohd Khalid Ansari who said there is no chairperson in NCMEI since the previous incumbent demitted office in December 2014.
It further said that without the chairperson, all orders passed by the commission are liable to be set aside as being of no legal consequences and void ab initio (to be treated as invalid from the outset).
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To which the bench asked the Centre to produce details of all decisions taken till date by the commission in absence of the chairperson.
It also said the appointment should be done in accordance with the NCMEI Act.
The court has now fixed the matter for further hearing on October 16.
The NCMEI Act came into effect from November 2004 and in January 2005 the central government issued the notification identifying Muslim, Christian, Sikh, Buddhist, Zoroastrian (Parsis) communities as minorities for the purpose of the Act.
The commission was established to protect and safeguard the educational institutions which are established by the minorities in India and also to ensure rights of minorities to establish and administer educational institutions of their choice.