They are under a vulnerable classification by the International Union for Conservation of Nature but are part of the illegal exotic pet trade.
A fourth species of turtle found in the luggage, a red-eared slider turtle, is a common pet, according to CNN.
They had come in on a flight from Hong Kong, where poachers trap turtles, despite laws that protect the vulnerable animals.
Last year the Philippines customs officials seized 560 different species, including 250 geckos, 254 coral snakes and other reptiles, CNN reported.
So far this year, it has seized 63 iguanas, chameleons and bearded dragons.
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