The Indian Church Act of 1927 established the legal union between the Church of England and the Church in India, but this was repealed in 1960 without an alternative act being established. As a result, most Indian churches registered as societies under the Societies Registration Act of 1860 rather than the Religious Endowments Act of 1863 or Charitable and Religious Trust Act of 1920. This means that technically, churches are considered voluntary NGOs rather than religious charities under Indian law.

1. Legal Status of Churches in India – a journey since the revocation of the Indian Church Act, 1927
Mangneo Lhungdim
On the 22nd of December 1927, The Parliament of England passed an enactment known as the Indian Church Act of 1927. The Indian Church Act, 1927 (17&18 Geo.5, CH.40) makes the provision incidental to and consequential on the dissolution of the legal union between the Church of England and the Church of England in India, and the Church of England in Ceylon.
The Indian Church Act, 1927 was repealed in December 1960 by section 2 of the British Statutes (Application to India) Repeal Act, 1960.
After fifty four years, the effect of this repeal has never been reviewed and re-examined. However, the intention of the Central Government was to ensure that the rights of ‘possession, control and use’ which vested in the Indian Church Trustees in respect of the churches in the second schedule were not in any way interfered with or affected.
On May 11, 1957, when the Fifth Report of the Law Commission (chaired by M.C. Setalwad) was submitted to the then Law Minister Shri Ashok Kumar Sen, one of the members Dr. NC Sengupta had a difference of opinion and signed the Fifth Report of the Law Commission only under the condition that the commission agreed to include his Note as annexure. In his note, Dr. Sengupta recommended to the GoI to set up an alternative legislation for governance of Indian churches in place of the repealed Indian Church Act, 1927.
No alternative act has come about ever since which can be regarded as specific to governance of the Church in our country.
Interestingly, most of the existing Indian Churches established post revocation of the Indian Church Act subscribe to the Societies

2. Registration Act, 1860 (including various States amendments) even in the face of other alternatives such as the Religious Endowments Act, 1863 or The Charitable and Religious Trust Act, 1920.
Churches or faith-based organizations across North East India including in majority Christian states such as Mizoram, Nagaland and Meghalaya chose to register themselves as societies under the societies registration Act. I have not come across any research or article explaining why our churches have not registered as ‘religious charities’ under the Religious Endowment Act or the Charitable and Religious Trust.
Thus, technically speaking under Societies Registration Act our churches are voluntary ‘NGOs’ and cannot be called a religious charity. SRA 1860 is not meant for religious charities. Now, to be considered a ‘NGO’ is not as simple as one might often think. As a legal entity, NGOs are bound by all conceivable legal and statutory compliance as that of any establishment.
Under the SRA 1860 definition, there is no different treatment between a ‘church’ from that of Vishva Hindu Parishad (VHP) or the Board of Control for Cricket in India (BCCI).