More than 3,700 pig-nosed turtles and nearly 900 snake-necked turtles were found at the weekend, hidden in containers in a building on the outskirts of the capital Jakarta.
"Customs officials succeeded in foiling an attempt to smuggle turtles," said a statement from Jakarta airport customs office. The turtles were reportedly due to be sent through the airport, and airport customs officials succeeded in stopping the smuggling bid.
The turtles, worth an estimated USD 90,000, were concealed among clown loach fish, which can be legally exported from Indonesia.
The International Union for Conservation of Nature classifies the pig-nosed turtle as vulnerable and the snake-necked turtle as critically endangered, and says both species are popular as pets.
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Some turtle species are also popular in China as exotic food or for use in traditional medicine.
Indonesia, a tropical archipelago of more than 17,000 islands, is home to a kaleidoscope of exotic animals and plants, but the illegal trade in wildlife is rampant and laws aimed at providing protection are often poorly enforced.
Numerous endangered species, from the Sumatran elephant to the Javan rhino, have been driven to the brink of extinction, with poachers targeting them for their body parts for use in traditional medicine.