The reptiles, which were alive and duct-taped, were possibly abandoned at NAIA Terminal 2 due to the Philippines' strict policy on illegal wildlife trading, CNN Philippines reported.
The animals were discovered on Sunday by the country's Bureau of Customs at Ninoy Aquino International Airport.
Among the animals found were the Indian Star Tortoise, classified as "vulnerable" by the International Union for Conservation of Nature.
More than 1,500 turtles and tortoises were found in four discarded suitcases. Authorities believe a Filipino passenger may have been "informed of the vigilance of Bureau of Customs against illegal wildlife trade and its penalties" and so decided not to claim the four suitcases upon arrival.
The 1,529 turtles were turned over to the Environment Department on Sunday.
Both types of animal are often kept as exotic pets, but are sometimes also used as a form of traditional medicine or served as food across parts of Asia.
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.
Some people consider their meat to be an aphrodisiac.
Discoveries of smuggled wildlife are not uncommon in the Philippines.
Last year, the agency said, it seized a total of 560 different exotic species that were packed into parcels, luggage and shipments.
The large seizure comes just one week after smugglers were arrested in Malaysia with 3,300 endangered pig-nosed turtles aboard a boat.