St Martin's Hall, in Northumberland St, Northeast Valley, and Holy Cross Church, St Kilda, have both been shut after structural reports found they were not up to code.
Diocesan manager Graeme Sykes said the church was working through a process of figuring out what needed to be done with the buildings.
This involved discussions with the affected communities, which had already begun informally at a parish level.
Holy Cross Church was built on an unstable sand base and would be extremely expensive to repair and strengthen.
It was likely that it would need to be demolished, Mr Sykes said.
The Northumberland St hall was used by many community groups and its fate would be discussed with them before anything was done.
''If there is enough support it could be repaired,'' Mr Sykes said.
The diocese owned about 70 buildings, about half of which were in Dunedin.
These buildings had been assessed and Mr Sykes said it was unlikely there would be more closures except possibly in rural areas with buildings that were hardly used any more.
One community group that used St Martin's Hall was the St Martin's Friendly Flea Market, which has held 11 markets a year in the hall since 1978.
The market organising committee decided to discontinue the market after the hall was closed.
Although the hall closure was the main reason for ending the market, declining stall and patron numbers were also factors.
Founding member Jean Marchant said the market had been very successful when it started.
Once there had been a waiting list for stalls but over the years weekend trading and an increased number of op-shops had made it harder to compete.
Many other community groups, including the Guides and Brownies, an indoor bowling club, and table tennis club, also used the hall and it had often been hired out for functions.
''The hall has a lot of memories for a lot of people,'' Mrs Marchant said.
''I'm sad to see it closed.''
