Representatives from the Anglican, Catholic and Uniting churches on Wednesday fronted the Yoorrook Justice Commission in Melbourne.
During the hearing, it was revealed the Anglican Church's property trust holds an estimated 260 hectares of land in Victoria.
That equated to about $1.49 billion worth, with the Melbourne diocese alone holding $1.38 billion of that total value, and not accounting for improvements to the land or any buildings on it.
Yoorrook counsel assisting Tim Goodwin flagged the government would have given some of that land to the church without regard for Aboriginal people, and there was no traditional owner group with land of such a value.
"There's no question that there's an incredible disparity of land justice outcomes between the Anglican church and First Nations Victorians," Anglican Bishop Richard Treloar of the Gippsland diocese, said.
Commissioner Tony North KC noted Yoorrook was only able to ask the Anglican church about its land ownership figures because both the Uniting and Catholic churches applied to keep their figures confidential.
The truth-telling inquiry was slated to determine those churches' 26 claims for non-publication orders over their submissions at a later date.
There was a "shattering silence" from the churches about what they were doing to set the actions of the past right, Mr North said.
All three churches revealed they did not have schemes to address land acquisition.
Bishop Treloar conceded the 1.5 per cent of land sale revenue the Gippsland diocese put towards Aboriginal ministry was "woefully inadequate".
However, the Anglican church would be guided by Yoorrook's recommendations about how compensation should be given to Aboriginal people for land injustice, the bishop said.
Bishop Treloar condemned the Anglican church's role in running missions, describing them as places of confinement based on a sense of cultural superiority and a responsibility to preach the gospel "completely ignorant of any pre-existent spirituality".
"There's this sort of 'protection' going on at one level and cultural genocide at another level and these two things are kind of co-existing," Bishop Treloar said.
"It's pretty hard to preach the gospel on stolen land."
The Anglican church set up and ran missions in Victoria including at Lake Tyers and Lake Condah.
Uniting Church moderator Reverend David Fotheringham acknowledged the church's involvement in missions contributed to Aboriginal people's dispossession from land, culture and language.
Archbishop of Melbourne Peter Comensoli stressed the Catholic church was not involved in missions but said the reality that they led to Aboriginal people's languages stopping was "deeply damaging".
He suggested the church's history with Aboriginal people was predominantly positive and enabled them to flourish, only marred by "individuals and localised communities".
Yoorrook's work will inform statewide treaty negotiations between the government and the First Peoples' Assembly, slated to begin later this year.
