The case has been registered at Civil Lines police station here in Uttar Pradesh.
The accused have been charged with using fake documents to transfer properties belonging to Indian Church Trustees.
The complaint has been filed by Bishop John Augustine of the Lucknow Diocese of Church of India, Pakistan, Burma and Ceylon (CIPBC).
The complainant has said that in 1970, some Bishops of Church of India had constituted Church of North India Trust Association. Later, using fraudulent means, the post of Bishop of Calcutta was created.
"The same people in 1991, spread this fake organisation and transferred the properties belonging to Indian Church Trustees, worth Rs 1000 crore, to the Church of North India Trust Association," the complainant said.
Those named in the complaint are Bishop Peter Baldev, P.C. Singh, P.P. Marandi, P.K. Samanto Roy, general secretary Alwin Masih, Jayant Agarwal, Pal Dupahre, P.P. Habil, Suresh Jacob, Rajiv Chand, A.R. Stephen, H.R. Mal, Marvin Masih, Prem Masih, Ashok Vishwas, Prabal Dutta and Shashi Prakash.
The transferred property includes church properties on Mahatma Gandhi Marg Lucknow and in Allahabad.
The accused have reportedly shared Rs 10,000 crore among themselves.
A senior police official in Allahabad said that the case has been registered and investigations have begun.
"The investigations will need time since the range is rather wide. If the allegations are found true, this could be one of the biggest church scams in recent years," he said.
( With inputs from IANS )