The species included star, redfoot and sulcata tortoises as well as red-eared terrapins and were worth 4.5 million Philippine peso (£65,623) on the illegal wildlife market.
The reptiles will now be looked after by the national Wildlife Traffic Monitoring Unit, while the airport continues to crackdown on illegal wildlife trade.
The creatures were discovered squirming in four bags when they were run through the X-ray machine at Ninoy Aquino International Airport. One picture shows a turtle taped up and tucked inside a trainer.
Three of the species found are classified as vulnerable by the International Union for Conservation of Nature.
Customs officials made an unusual discovery in the Philippines on Sunday - over 1,500 live turtles stuffed into suitcases.
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Antiporda added the Philippines would ask Chinese authorities whether they wanted to take back the confiscated turtles which were being quarantined and treated in Manila.
It is not the first time staff at the airport have encountered passengers of the reptile variety.
Turtles and tortoises are kept as exotic pets, but are also used in Traditional Chinese Medicine and considered a delicacy.
Animal smuggling carries a penalty of up to two years in jail and a 200,000 peso (Dh14,000) fine in the Philippines.
Last week, 3,300 pig-nosed turtles were smuggled into Malaysia by boat - though this attempt was intercepted by Malaysia's maritime agency.