The 80- to 100-year-old tree came down at about 10am during removal works on Speargrass Flat Rd, taking the 55-tonne capacity machine with it, and closing the road.
Constable Terry Erceg, of Queenstown, said the "very, very lucky" operator - a 51-year-old Cromwell man - was taken to the Lakes District Hospital with just a dislocated shoulder.
"OSH is investigating the matter now," Const Erceg said.
"They were removing the dangerous trees at the time, but what actually caused the tree to fall I don't know."
He said the operating cabin of the crane was crushed where the truck had fallen on to its side and had extensive damage to the boom, but otherwise seemed fine.
The Otago Daily Times believes it had been lowering the black poplar down before the tree pulled the crane over with it.
Queenstown tree-care firm Tricky Trees, in conjunction with Christchurch-based crane contractors Smith Crane and Construction, was carrying out the removals on behalf of private landowners.
Tricky Trees director Tim Bolt said the tree, which was reportedly on a lean before its attempted removal, had been condemned by the Queenstown Lakes District Council.
He did not wish to comment on how the accident happened.
A spokesman for Smith Crane and Construction could not be contacted, but another crane is on its way from Lake Benmore to pull the machine back on to its wheels.
A man was killed on nearby Lower Shotover Rd in 2009 when a rotten poplar fell on his ute during high winds, prompting investigation and condemnation of trees along the road.
