Hi hardworking dad,
Sorry to learn about your situation.
In my best knowledge, your wife has every right to do whatever with herself, she can move back to her country tomorrow and the court/police would not care.
However, where the child goes is an entirely different story. Given the child is born in Australia of an Australian citizen and if the child is an Australian citizen (can you please confirm if you are a citizen as your child- remember citizenship in Australia is not always a birth right), where the child lives is dependent on the decision of both parents, and in the case when the parents have split up (divorced, separated or simply broken up) then it is the decision of the family court.
How the family court decides on custody is wholly merit based- best interest of the children. If you want full custody, it is very extreme and you'd have to prove that the mother is utterly unfit e.g. she's a drug addict. Say if the court gives you 50-50%, or even say, you 2 days a week, she gets 5 days, both of you are required by law to stick to the parenting order or can be penalised for opposing a court order. The child cannot go interstate, let alone overseas even for a holiday without permission of both parents. If one parent unreasonably oppose, the other can take he/her to court.
Worst case is, she takes the child without permission back to Philippines, it will be considered criminal kidnapping. AFP may try and extradite her or have her arrested the moment she returns to Australia soil. I have known of a parent who took the kids to a country with no extradition treaty. I didn't know that couple well but the one left behind was devastated.
Hope I hadn't alarm you. Best thing for you to do is try and negotiate calmly with her. Going to court is last resort and costly and don't expect that it can be sort out in weeks or even months. If you had to go down that path, talk to a family lawyer asap.
Good luck and stay calm. Don't forget to rejoice the fact that you are a daddy!!!