The wildlife included 11 tarsiers, 11 snakes, 11 monitor lizards, eight sailfin lizards, eagle owls and scops owls.
They were found on Thursday, packed in styrofoam cases which were labelled as aquatic plants, said Theresa Mundita Lim, head of the country's biodiversity bureau.
"We received a tip last January. That is when we began our surveillance. We already observed (the suspect) going back and forth to the airport," transporting items for shipping, she told AFP.
He has been arrested for violating wildlife laws and could face four years in jail, Lim said.
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She said that while birds like cockatoos had previously been found being smuggled through the airport, this was the first time they had found tarsiers, one of the world's smallest primates, hidden in an airport shipment.
The Philippine tarsier is listed by the International Union for Conservation of Nature as "near-threatened."
Other species like the sailfin lizard and the eagle owl are listed as "vulnerable," meaning they are at risk of extinction in the wild.
Last year charges were filed against six airport police officers for allegedly planting bullets in luggage and then demanding extortion payments from the victims to avoid arrest.