The bags contained several varieties of exotic turtles, including red-eared slider turtles and star, redfoot and Sulcata tortoises.
The Filipino traveller who owned the bags left them unclaimed in the arrivals area, but could face a prison sentence of one to two years or a fine of between £291 and £2,916.
On Sunday, customs agents found 1,529 turtles and tortoises inside the unclaimed suitcases, which were likely left behind by a passenger traveling from Hong Kong to Ninoy Aquino International Airport.
The 1,529 exotic turtles were worth an estimated 4.5 million Philippine pesos on the black market - that's about $86,750 US dollars.
The reptiles will now be looked after by the national Wildlife Traffic Monitoring Unit, while the airport continues to crackdown on illegal wildlife trade.
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Some of the turtles had also been found wrapped in duct tape, packed within plastic bins.
It's not clear why that passenger abandoned the animals in the airport, though the customs bureau has a guess: "The passenger may have been informed of the vigilance of the port against illegal wildlife trade and its penalties".
Tortoises are land animals while turtles can be aquatic or terrestrial.
It's not the first case involving exotic animals at the airport.
"Earlier this year, 63 Iguanas, Chameleon and Bearded Dragons were also intercepted through the efforts of vigilant frontliners and operatives of Customs", the agency added.