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A division bench of Chief Justice Antony Dominic and Justice Dama Seshadri Naidu issued the stay while considering a plea filed by the Cardinal against a single bench order directing police to register an FIR in the case.
Staying further investigation, the court directed police to maintain status quo in the matter.
Last week, the single bench had passed the order on a petition filed by Shine Varghese from Cherthala.
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Besides Alencherry, the others against whom the complaint was lodged were priests Joshy Puthuva and Sebastian Vadakkumpadan and middleman Saju Varghese.
Following the single bench order, the police had registered a case against them.
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 three others in sale of land worth crores of rupees belonging to the archdiocese.
Alencherry, who is also the major Archbishop of the archdiocese, is the first accused in the case, police said.
They were charged under various sections of the Indian Penal Code, including 120b (criminal conspiracy).
Moving the division bench against the single bench order, the Cardinal said the property transactions the archdiocese had were not in conflict with the applicable laws of the land or canon laws.
Under canon law, the Archbishop has the power and authority to administer properties of the archdiocese.
Cardinal Alencherry also claimed that the writ petition was disposed of by the single bench without issuing any notice to the respondents and serving a copy of the plea.
An opportunity to file a counter affidavit was denied. “This tantamounts to violation of natural justice as well as the applicable rules,” the Cardinal submitted.
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 inquiry 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 panel, comprising priests, was appointed by Alencherry, who is also the Major Archbishop of the archdiocese, after some priests and faithful accused him of selling prime land of the archdiocese for “a very low price.”
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.