Paul Dean Davy, 53, was shot in the back of the head while talking to another Australian man at the Blue Rock Beach Resort restaurant in Olongapo, north of Manila, on Friday night, News Limited reports.
Mr Davy, from Brisbane, was the general manager of resort.
Fairfax on Sunday quoted senior officer Tyrone Tecson, of Olongapo police, as saying a witness had told of Mr Davy talking to another Australian man at the restaurant when he was approached from behind and shot at point blank range in the back of the head.
"When we arrived, still there were lots of customers," Mr Tecson was quoted as saying. He indicated that Mr Davy knew his attacker.
It is understood the restaurant was full of holiday-makers and families at the time.
Mr Davy was rushed to hospital but later died.
Police are describing the shooter as a Filipino man aged 30 to 35 wearing a blue cap and clear prescription glasses.
An Australian Department of Foreign Affairs and Trade spokeswoman has confirmed "the death of a 53-year-old man in the Philippines".