The Transitional Cathedral will remain the property of the Anglican Diocese of Christchurch when the parishioners from the church, once based there, cut diocesan ties over its stand on same sex marriage.
Diocesan manager Edwin Boyce said the Latimer Square site and Transitional Cathedral belong to the parish that remains part of the diocese.
"While clergy and a large number of parishioners have decided to disaffiliate, the parish still remains in existence."
Parishioners from four Christchurch churches will cut ties with the diocese in three months after the Anglican Church voted to allow the blessing of same sex marriages.
One of those is St John's Latimer, which was based on the site where the Transitional Cathedral now stands.
St John's stone church and hall was demolished after the February 22, 2011, earthquake and the diocese decided to build the temporary replacement for the Christ Church Cathedral on the site with the intention St John's would return eventually.
St John's Latimer has since been based on Berwick St, St Albans.
"The Transitional Cathedral will continue to be used by the Cathedral until the Cathedral reinstatement in the Square is complete, at which point it reverts back to the parish," Mr Boyce said.
He said a meeting with St John's had not yet taken place to work out its exit strategy, so he was unable to comment on where the people from the church would be based.
St John's Latimer's Reverend James de Costobadie said the congregation would continue to be based at Berwick St for the "foreseeable future."
"We will need to change our name, as we will no longer be the Parish of St John's, but have not selected one yet."
He said they were disappointed to be disaffiliating but would maintain a good relationship with the diocese.
"It is a great sadness for us that the national Anglican Church is on a journey where we do not feel able to follow, which means we felt we had no option but to choose to disaffiliate from the diocese."
Parishioners from St Stephen's Shirley, St Saviour's and St Nicholas' in South Christchurch and St John's Woolston are also disaffiliating with the diocese.
Mr Boyce said the exit process would take about three months for logistics to be sensitively managed in a respectful and orderly way.
"In some cases it was acknowledged that although the majority of the people attending these churches intended to leave, some will remain."
He said the diocese was committed to care for those remaining, and to enable a smooth exit for those choosing to leave.
Mr Boyce said further meetings were still being arranged to work out exit strategies to do with personnel, plant, buildings, bank accounts and more.
He said it was agreed decisions about these things would happen on a case-by-case basis depending on particular circumstances and fairness.