Drink the readily available bottled water. Buko (young coconut) juice is also safe if they have not added local ice to it. Be wary also of Buko juice vendors, some usually just add sugar to water. Buy and eat fruit that has not already been cut up. Cooked food from a karenderia (outdoor canteen) is okay if there is a fire under the pots and the food has been kept hot.
If you must drink tap water (it is usually served/contained in a small to medium plastic bag), water in Manila, Cebu City, Olongapo-Subic, and Angeles may be ok, but it is recommended that you boil tap water for at least 5 minutes just to be safe. Elsewhere drink bottled water. There is always the risk of contracting amoebiasis when drinking tap water in the countryside. Also, this applies to ice that is usually put in beverages.
Bottled water is best purchased from within stores and sheltered eateries. Bottled waters sold outside (by the roads) are more than likely used bottles filled with tap water, sealed then cooled.
CDC advises that risk of malaria exists in areas below 600 meters, except for the provinces of Aklan, Bilaran, Bohol, Camiguin, Capiz, Catanduanes, Cebu, Guimaras, Iloilo, Leyte, Masbate, northern Samar, Sequijor, and metropolitan Manila. NB: chloroquine is no longer a recommended malaria preventative for anywhere in the Philippines. In general malaria is not common in the Philippines and around half of the c. 40,000 annual cases are in a couple of discreet locations.
Also please note the tubercolosis is very common in the countryside, it is advisable not to stay in certain villages in areas you are not familiar with for a very long time. It is also higly advisable that if one coughs or is looks weak in strength it is highly advisable to avoid contact to that person. Bring anti-diarrheal drugs with you, as unsanitary conditions present a high risk for traveler’s diarrhea.