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A blaze at a historic Antarctic hut which was Sir Edmund Hillary's favourite place to stay at Scott Base has destroyed a piece of Kiwi history.

The A-frame hut went up in flames on Saturday night after a fuel leak from a heater.

Staff desperately tried to douse the fire in temperatures as low as -35C.

The hut, described by Antarctica New Zealand chief executive Lou Sanson as part mountain hut, part bach, was on the Ross Ice Shelf, and looked up at Mt Erebus.

"It's about 20 minutes away from Scott Base, but far enough away to get that real feeling of being in Antarctica," Mr Sanson said.

"It's just the most stunning wilderness experience. You'll never replace the character of that place."

About 12,000 New Zealanders have stayed in the hut while doing survival training.

Many scientists, artists and politicians, including Prime Minister John Key and Labour Party leader Phil Goff, have also stayed there.

The hut was Sir Edmund Hillary's favourite place to stay in Antarctica, and the New Zealand explorer stayed in it during his last trip to the ice, in January 2007.

The building became a training base after it was abandoned by US researchers at the McMurdo Station in 1971.

"The A-frame represented something uniquely Kiwi in Antarctica," Mr Sanson said. "It was the concept of a mountain hut mixed with a bach and it said something about who we are.

"It will be sadly missed by all those who have been part of the New Zealand programme in Antarctica over the past 38 years."

Scott Base staff had changed diesel fuel tanks at the hut, and were re-lighting the heater when leaking priming fuel ignited. The fire quickly destroyed the timber and bitumen building.

Mr Sanson said he was extremely thankful that no one was seriously injured in the fire.

"It is a testimony to the skill of our staff that they were able to think quickly and remove themselves from harm.

"Fire is the biggest hazard in Antarctica. Earlier this season, two Russians were killed when one of their buildings burned down."