Australia allocated close to $40 million towards helping the Philippines counter Islamic militants and the threat of returned foreign fighters from the Middle East.
The Defence Force has 80 soldiers training Filippino troops in urban warfare, and also had surveillance aircraft and some navy personnel deployed as part of a mission dubbed Operation Augury.
Overall, there are 100 Australian military personnel in the Philippines, with patrol boats HMAS Albany and Glenelg doing maritime surveillance with Philippines Naval Forces in Sulu and Celebes Sea.
This year's federal budget did not disclose money allocated over the next four years and references to the operation have disappeared from the department's website, with the Turnbull government citing "national security reasons".
Defence secretary Greg Moriarty told a Senate estimates hearing on Tuesday $39.1 million had been allocated in the 2017/18 financial year and as of the end of April, Defence had spent $7.6 million.
He said not all costs had been captured.
Last year, the Philippines scrambled to quash a five-month Islamic State insurgency in Marawi.
