The Hevilift twin otter aircraft carrying nine people came down near Mount Lawes, about 20 kilometres north of the capital Port Moresby, on Saturday morning.
The Australian man was killed along with the co-pilot and a passenger, both of whom were PNG nationals.
The survivors, all PNG nationals, were taken to a hospital in Port Moresby.
In a statement, Hevilift said it would be "conducting a thorough investigation" and was "cooperating with all relevant authorities to determine the cause".
"Hevilift’s thoughts and sympathy go to the families of those who have died in the crash and the company will continue to provide every assistance to the survivors," it said.
The flight had been travelling from Woitape in Goilala district to Port Moresby.
William Seneka, a senior investigator with PNG's Accident Investigation Commission, said the cause of the crash was yet to be determined but it was likely that bad weather was a significant factor.
"There was low clouds from speaking to some aircraft that flew in this morning, and it's been raining," he said.
The Department of Foreign Affairs and Trade said it was providing consular assistance to the family of the Australian.
More than 20 planes have crashed since 2000 in PNG, where the rugged terrain and lack of internal connecting roads makes air travel crucial for around 6 million citizens.
In July 2012, a helicopter, also operated by charter company Hevilift, crashed while flying from a drill rig site to Mount Hagen in the Western Highlands, killing two Australians and a New Zealander.
In one of the worst accidents, an Airlines PNG Dash-8 crashed 20 kilometres south of Madang in October 2011, killing 28 of the 32 people on board.
In June this year, the Accident Investigation Commission found that pilot error was a contributing factor in that accident.
Map: The Hevilift twin otter aircraft was heading from Goilala district to the PNG capital, Port Moresby.