Unfortunately, the Hague Convention governing civil aspects of international child abduction is not yet in force between Israel and the Philippines.
The Philippines acceded to the convention on 29.3.2016 , with it becoming a "Hague Convention" Country only on 1.6.2016. At present, only Japan has accepted its accession, so currently the Hague Convention is only relevant regarding abductions between Philippines and Japan, though hopefully, other countries, including Israel, will accept the accession, so that it will have wider effect.
Currently, therefore, you would need to take direct legal action in the Philippines via experienced specialist counsel there, for a non-Hague order for the return of your child and/or to represent you in custody proceedings there, if perhaps already initiated by your wife. You would be advised to select counsel in the Philippines who would work in conjunction with English speaking specialist family law counsel, in Israel, to maximize your representation and thereby improve your chances of returning your child.
Our law practice could, for example, offer such assistance, and provide an expert legal opinion on Israeli family law , to be presented overseas, to explain about your equal parental rights under Israeli law and the independent rights of the child (who is an Israeli citizen, too) , and how they have been breached. We could, also assist in the preparation of detailed affidavits, and gathering relevant evidence, regarding habitual place of residence and joint parental intentions.