The FIR was registered nearly a week after the Kerala High Court ordered the police to do so against the cardinal, priests Joshy Puthuva and Sebastian Vadakkumpadan, and middleman Saju Varghese on a petition filed by Shine Varghese from Cherthala.
Shine had moved the high court, saying that the Ernakulam Central Police had not registered an FIR on his complaint against the cardinal and others over the land deals.
They were named in the complaint alleging criminal conspiracy, criminal breach of trust and cheating in sale of over three acres of land, worth crores of rupees, belonging to the Ernakulam-Angamaly Archdiocese.
Alencherry, who is also the major archbishop of the archdiocese, is the first accused in the case, police said.
They have been charged under various sections of the Indian Penal Code (IPC), including sections 120b (criminal conspiracy), 405 and 406 (criminal breach of trust),and 420 (cheating and dishonestly inducing delivery of property), police said.
Police also secured legal advice before registering the FIR.
The cardinal and the other accused moved separate appeals in the high court, submitting that the order of the single judge and the conclusions arrived at by him were unsustainable in law and facts.
Earlier, a six member church committee, which probed the alleged irregularities, said it had found numerous instances of violation of canon and civil laws.
It had recommended necessary action against those responsible.
The committee also said the cardinal "seems to have fully known and involved" in alienation and purchase of lands by the archdiocese between April 1,2015 and November 30, 2017.
The panel, comprising priests, was appointed by Alencherry.
A group of priests of the Ernakulam-Angamaly Archdiocese had took to streets last week, urging Alencherry to keep off all responsibilities of the archdiocese in view of the high court order to launch a police probe on alleged irregularities in a land deal involving him.
A meeting of over 200 priests had also urged police to commence a probe after registering an FIR against Alencherry and others on the complaint over the alleged irregularities.
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