You can register your NGO either as a trust, society or private non profit company and the procedure for registration will accordingly vary. For trust, register it under Indian Trusts Act 1882 and file your application for the registration depending upon the jusridiction (area) you seek to establish the trust in.
If it is a society then section 20 of societies registration act 1860 will apply and applicationn for registration can be made at the district or state level at Registrar of societies office.
If it is in form of a company then section 8 of Companies Act 1956 will be applicable and application has to be made to Registrar of companies office. The procedure here is slightly more elaborate and requires various documentation like declaration of assets, sound mind of people involved, reasons for establishing etc.
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