Passing the order, Justice B Kemal Pasha rejected the Cardinal's contention that the land belonged to the diocese and that a third party could not complain about the alleged loss in the sale of such a private property.
He held that the Cardinal was only a caretaker of the assets owned by the church and that any ordinary member of the society could seek action if any irregularities took place in the dealings of the Church properties.
Besides Alencherry, priests Joshy Puthuva and Sebastian Vadakkumpadan and middleman Saju Varghese were the others against whom the complaint was lodged.
The judge observed that the non-registration of the FIR, despite receiving a complaint, was in violation of the Supreme Court's 2013 ruling in the Lalita Kumari case, laying down the guidelines on FIRs.
Directing the police to conduct a free-and-fair probe after filing the FIR, Justice Pasha said the alleged conspiracy and breach of trust issues could be investigated.
In his complaint, the petitioner had sought the registration of an FIR for criminal conspiracy, criminal breach of trust and cheating against the Cardinal and the three others.
The complaint was filed last month after a church committee, which probed the alleged irregularities in financial and land transactions of the archdiocese, said it found numerous instances of violation of canon and civil laws and recommended necessary action against those responsible.
The six-member enquiry committee had also said that Cardinal Alencherry "seems to have fully known and involved" in the alienation and purchase of lands by the archdiocese between April 1, 2015 and November 30, 2017.
The Syro-Malabar Church has over 30 dioceses in the country and four outside -- in the US, Canada, Australia and Britain -- serving over five million faithful.
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