A passenger, who the authorities said was a Filipino national, abandoned the animals in four items of luggage in the arrivals area before security checks, after arriving at Manila on a flight from Hong Kong.
"The passenger may have been informed of the vigilance of Bureau of Customs against illegal wildlife trade and its penalties," the Bureau of Customs NAIA announced in the statement, which was posted on Facebook.
A number of different breeds were discovered among the turtles and tortoises, including Star Tortoises, Redfoot Tortoises, Sulcata Tortoises and Red-eared Slider turtles.
The illegal trade of wildlife carries strict penalties in the Philippines. Violators face fines up to 200,000 pesos ($4,000) and two years in prison under the country's Wildlife Resources Conservation and Protection Act.
In their announcement, the Bureau of Customs NAIA released a series of photos of the smuggled turtles, some of which had been bound in duct tape.
"BOC NAIA will continuously protect the borders against importation and exportation of illegal wildlife trade and other prohibited and anti-social goods," the bureau said.
All of the animals were turned over to the Wildlife Traffic Monitoring Unit of the Philippines Department on Natural Resources, the Bureau of Customs PH said.
The case follows a similar bust by Malaysian authorities last week when 3,300 rare pig-nosed turtles worth around $36,909 were discovered being smuggled into Malaysia from the Indonesian island of Papua, according to Reuters.
The illicit trade in turtles and tortoises is a multi-million dollar annual industry, according to the Wildlife Justice Commission, a Netherlands-based animal welfare organization.