A house at one of Otago's most significant heritage locations has been destroyed by fire.

A Fire and Emergency New Zealand spokesman said crews were notified of a fire at Matanaka Farm in Matanaka Rd near Waikouaiti, at about 3.15 pm yesterday.

The farmstead which burned down is understood to have been constructed on the original location of whaler Johnny Jones' homestead. Jones owned the property from 1838 to 1869.

When firefighters arrived they found the homestead at the heritage attraction and active farm "well-involved" with a significant fire.

There was a partial collapse of the two-storey residential house as crews with hose reels began an external attack.

Last night, a crew was dampening down hot spots and a fire investigator was at the scene.

It was too early to indicate any cause for the blaze, the spokesman said.

Firefighters work to extinguish a blaze at a house which caught fire at a historic farm at Matanaka yesterday. Photo / Gregor Richardson

Appliances from Willowbank, Waikouaiti, Waitati and Palmerston attended, along with tankers from Hampden, Waikouaiti, Waitati and Wakari stations.

At the scene, fire crews could be seen hosing the sizeable blaze using hose reels while smoke and steam billowed.

A St John ambulance was on hand as a precaution.

Heritage New Zealand (HNZ) southern area heritage assets manager Jess Armstrong said the building was not listed as a historic place.

She was "devastated" for the homeowners.

HNZ owns several category one historic buildings which were unaffected at the historic site, which is in private ownership, she said.

The farm at Matanaka is believed to be New Zealand's first European-style farm with New Zealand's oldest surviving farm buildings.

The house in better days. It is on the site of whaler Johnny Jones' original homestead. Photo / Gillian Vine

Australian entrepreneur Johnny Jones, a ship-owner, whaler and trader, purchased a whaling station and land at Waikouaiti in 1838.

After passing through several owners, Matanaka's farm buildings were given to HNZ in 1976.

- Oscar Francis and Hamish MacLean, ODT