Senator Wong said search and rescue teams reached the site of the crash - at one of the nation's most active volcanoes - overnight and there were no survivors.
Two Australians and two Filipino pilots were on board the Cessna 340, which lost contact after take-off from Albay province southeast of the capital on Saturday morning on its way to Manila.
The Australians on board were working as consultants for Energy Development Corp, a large geothermal power company.
"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.
with Associated Press
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