The National Commission for Minority Educational Institutions Act 2004 (2 of 2005) as amended by the NCMEI (Amendment Act 2006) lays down rights of Minority Educational Institutions as under:-
 
Right to establish a Minority Educational Institution:-

1. Any person who desires to establish a Minority Institution may apply to the Competent authority for the grant of no objection certificate for the said purpose.
    
2. The Competent authority shall:-
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   • On perusal of documents, affidavits or other evidence, if any; and
      
   • After giving an opportunity of being heard to the applicant, decide every application filed under sub-section (1) as expeditiously as possible and grant or reject the application, as the case may be:
     
     Provided that where an application is rejected, the Competent authority shall communicate the same to the applicant.
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3. Where within a period of ninety days from the receipt of the application under sub-section (1) for the grant of no objection certificate:-
    
   • The Competent authority does not grant such certificate; or
      
   • Where an application has been rejected and the same has not been communicated to the person who has applied for the grant of such certificate,
     
     It shall be deemed that the Competent authority has granted a no objection certificate to the applicant.

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After obtaining minority status certificate, the institutions have the following rights in terms of Article 30 (1) of the Constitution and Section 2(g) of the NCMEI Act. 

1. To choose its governing body in whom the founders of the institution have faith and confidence to conduct and manage the affairs of the institution.
    
2. To appoint teaching and non-teaching staff.
    
3. To admit the students of its community.  Non-minority students cannot be forced upon it.  Neither the policy of reservation on admission can be enforced by the State nor any quota or percentage of admissions can be carved out to be appropriate by the State in a minority education institution.  But if the institution is receiving any financial aid from the State then Sub-Article (2) of Article 29 of Constitution obligates the management to admit non-minority students to a reasonable extent. 
    
4. To receive a reasonable fee structure of it’s own. 
    
5. To take disciplinary action against  any member of it’s erring staff. 

It has been held by the Supreme Court in Case of P.A. Inamdar  Vs. State of Maharashtra [2006 (6) SCC 537] that: 

1. The policy of reservation in admission cannot be made applicable to a minority  institution. 
    
2. The policy of reservation in employment can not be made applicable to a minority institution. 

Further, a minority educational institution covered under Article 30(1) of the Constitution including a Madarsa is exempted from the purview of the Right of Children to Free and Compulsory Education Act.