However, their ages and nationality had yet to be confirmed, he said.
Stuff reports that the two children are brother and sister.
Ngāi Tahu Tourism runs the Shotover Jet and its spokeswoman Kirsty Phillips said the tree had fallen on the bank of the Shotover River, injuring five people who were sitting underneath it.
"All are believed to be conscious ... they are being assessed by emergency services and will be taken to hospital. The wellbeing of individuals is paramount and our focus is on supporting them, their whānau and our team."
A reporter at the scene said the large tree, which was beside the outdoor café area at the Shotover base, had fallen over with its roots completely ripped out.
There were park benches below the tree and it had fallen directly on at least one of them.
As well as the child taken in the chopper, the reporter said it looked like another child and an adult female had also been hurt.
"One guy was absolutely beside himself. The fire brigade and police had to hold him down basically," he said.
The Otago Daily Times reporter said it was "really windy" and gusts were blowing up dust across the site.
"You can barely stand up when a gust comes. You are pretty much cowering to the ground," he said.
Shotover Jet has issued an alert on its website saying that it is closed for the rest of the day.
Jimbo Paterson, owner of Mangy Moose Lodge near the Shotover Jet site, said there were now cones around the fallen tree.
Paterson said they had winds of up to about 50-knots gusting up the valley and big poplar trees were bending over - he was hoping they wouldn't go too.
A severe weather watch for northwest gales is in place in Central Otago and Southern Lakes.
The watch is in place from 1pm until 6am tomorrow and westerly winds may rise to severe gale in exposed places.
Metservice meteorologist Lisa Murray said observations at Queenstown Airport have shown mean wind speeds of 20km/h with gusts up to 52km/h.
Murray said there were places that could be more exposed to wind gusts that weren't under official observation.
A WorkSafe spokeswoman said they had been notified but the incident did not fall within their jurisdiction.
A Department of Conservation spokesperson said the tree was on conservation land, in an area subject to a commercial lease.
"We are currently determining who is responsible for maintenance of trees in this location. In the meantime, our thoughts are with those affected by this accident."