The Philippines is an archipelagic country that belongs to the biologically diverse Pacific Coral Triangle, rich in marine resources, including corals, reef fishes, and algae. This explains the continuous sustenance of the Filipinos on fish as a major protein source. Despite their contribution to human consumption, some commercially important coral reef fishes are a threat to food safety, compromising public health. Currently, ciguatera fish poisoning (CFP) has been focused on by scientists since it is the most frequently reported seafood-toxin illness in the world acquired from contaminated coral reef fishes. The present study investigates the contamination of reef fishes in the West Philippine and Sulu Seas using animal assay. Ciguatoxins (CTX) are present in commercially important reef fishes such as barracuda (Sphyraena barracuda), parrotfish (Scarus quoyi), rabbitfish (Siganus guttatus), grouper (Plectropomus leopardus), moray eel (Gymnothorax melanospilos), and snapper (Lutjanus campechanus). Scarus quoyi had the highest toxicity of 0.65 ± 0.55 ppb and 0.48 ± 0.36 ppb found in flesh and viscera, respectively. Although higher toxicities were observed from fish viscera, toxicities between fish parts did not vary greatly (p > 0.05). Positive samples exceeded the 0.01 ppb guideline established by the US Food and Drug Administration and the Philippines’ regulatory limit set by the Bureau of Fisheries and Aquatic Resources. Symptoms of mice showing the presence of Pacific CTX-1 were noted. Since mouse bioassay was used in screening reef fishes that pose non-specificity and insensitivity problems, the researchers suggest that analytical methods must be used in characterizing and quantifying these types of toxins. Establishing the methodologies in detecting CTX would greatly help monitor and manage CFP in commercially identified reef fishes in the country.