The fires are thought to have started about midnight on Friday, but firefighters and police had to wait until daylight to tackle the blaze.
At 2020m above sea level, the buildings are accessible only by chairlift or a 90-minute walk.
About 7.15am fire crews were airlifted into the area and used monsoon buckets, portable pumps and a portable dam to extract water from a nearby reservoir.
By 9.30am they were able to extinguish the fire that was still burning at the chairlift terminal building, but it was too late to save the chalet and the equipment shed.
A resident of National Park, the village at the base of the mountain, said she and her partner watched the fire after hearing alarms about 1.30am and noticing a red glow in the sky.
They drove along the main highway, from where the flames were clearly visible, towards the mountain.
"As we got closer and closer it was very dramatic - huge flames and great puffs of big black smoke every now and then," she said.
"We saw it wasn't just one fire, but two fires quite a way apart, and that's when we started to think it wasn't normal."
Police, who are appealing for witnesses, said it was unlikely the fires spread from one building to another because of the distance between them.
But spokeswoman Kim Perks said arson was unlikely to be confirmed until tomorrow.
Ruapehu Police area commander Inspector Steve Mastrovich said the investigators wanted to speak to anyone in the area on Friday afternoon and evening, including sightseers and employees.
Police would also check whether the 40-plus club lodges on the Whakapapa side of the mountain were occupied that night.
Dave Mazey, general manager of Ruapehu Alpine Lifts, the company that runs Ruapehu skifields Whakapapa and Turoa, said he had no idea who would want to damage the skifield.
He said he doubted rumours a disgruntled employee could be responsible.
"This is a lovely place to work and play. We don't even get graffiti up here, it's just not that sort of place."
Mazey was also perplexed by the lengths to which the arsonist went to to light the fires - it's presumed the culprit must have been on foot.
The chalet was open during the day on Friday and chairlifts were operating for summer sightseers. No people stay on the mountain overnight and Mazey said visitors and workers would have been off the slopes by 5pm. Police confirmed Whakapapa employees would be interviewed.
Although Mazey is devastated he was relieved the chairlift was saved.
He said the company has comprehensive insurance and was adamant Whakapapa would be open as usual when the ski season starts in June.
"The real effect is going to be that the sort of cafeteria and chalet facilities available at the upper levels of Whakapapa will be slightly less salubrious than they may normally be."
He anticipated temporary facilities would be in place this season but said both buildings would be rebuilt eventually.
The skifield is vital to the small communities of Whakapapa and National Park, and concern spread quickly through the townships yesterday morning.
"We're worried about whether they can get their insurance in time to reopen before the season starts, and what affect that's going to have on people's livelihoods," said the resident who witnessed the blaze.
Brian Stephenson, immediate past president of the Federation of Mountain Clubs, said the loss was deeply personal to many long-term users of the mountain.
Ski 150 club president Liz French said regular visitors felt the fires were a "personal assault".
"We're devastated. And we feel very much for RAL that they're going to have to deal with this."
- ADDITIONAL REPORTING: Nicola Shepheard
