Adviser Simon Chipperfield and consultant Karthi Santhanam were killed when the Cessna 340 crashed on Saturday morning.
Also killed were pilots Rufino James Crisostomo and Joel Martin.
The plane came down near one of the country's most active volcanoes shortly after taking off from Bicol International Airport on its way to Manila.
The Energy Development Corporation said it stood "in compassion and deep sorrow with the families of our fallen Kapamilyas in this unthinkable tragedy".
"We are working with authorities to bring them home to their loved ones where they may rest in peace," the company said in a statement.
"Our heartfelt sympathies go to their families and friends at this difficult time."
The company also offered its thanks to the rescuers, including the civilian volunteers, who helped with the search operation.
Foreign Minister Penny Wong confirmed the deaths of the two Australians on Thursday after search and rescue teams reached the crash site.
"On behalf of the Australian government, I wish to extend our deepest sympathy to the families of the two men Simon Chipperfield and Karthi Santhanam - both from Adelaide, my hometown - as well as the Filipino nationals involved," Senator Wong told reporters in Fiji on Thursday.
"The families of those who we have lost will be grieving and I express not only our sympathy and condolences, but to say to them, our hearts go out to them in this time of great grief."
Senator Wong also acknowledged the families of two soldiers killed during the search and rescue operation.
The soldiers were shot on Monday by five suspected communist New People's Army guerrillas in a market where they were buying supplies, military officials said.
Mr Chipperfield and Mr Santhanan both previously worked with oil and gas company Santos in Adelaide.
with Associated Press
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