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A drone will fly over the scene tomorrow morning to help determine the exact damage.
"It’s still standing, has received extensive damage in the upstairs area, the top storey," a Fire and Emergency New Zealand (Fenz) spokesman said.
The back of the building had also been damaged, there was extensive water damage, and the overall structural condition of the building was yet to be determined, officials said.
A Waimate local said they noticed smoke coming from the homestead about 2pm on Saturday.
They were called to the scene at 1.45pm, after reports of smoke coming from the two-storey building.
A Waimate local said it is "devastating" and "terrible" to see the historic homestead on fire.
The local was located up on a hill and could see "lots of smoke" coming from the homestead.
At its peak, eight fire appliances, a command vehicle and three water tankers fought the fire.
A Fenz spokesman said at 6.30pm that the fire had been largely extinguished by 5pm and mop up efforts, including checking for hotspots, was continuing.
Five appliances, the command vehicle and two water tankers remained on the scene, and a backup fire appliance from Timaru was being brought in.
Appliances would be progressively released from the scene throughout the evening.
A Waimate fire appliance would stand by at the scene overnight.
Because of the scale of the incident, the matter had been referred to the police, but the fire cause was currently viewed as undetermined rather than suspicious, a Fenz spokeswoman said.
A Fenz fire investigator had looked over the fire site, and further work would be undertaken tomorrow morning.
No one was reportedly injured. Te Kiteroa is a retreat that hosts workshops, talks, retreats and meditative experiences.
The homestead has seven bedrooms, two bathrooms and five ensuites and was build back in 1913.
Te Kiteroa was due to host a Heritage Festival from May 25 to May 30.
- Additional reporting John Gibb