Two men were also arrested after navy officers raided a warehouse near a port on Sumatra island late Tuesday, acting on a tip-off that it was being used to store the creatures which are also known as "scaly anteaters".
They discovered 223 live pangolins, 24 of the creatures which were already dead and frozen as well as nine large bags of pangolin scales, local navy spokesman Sahala Sinaga told AFP.
He said the total haul seized near the city of Medan, which was going to be sent to neighbouring Malaysia, was worth an estimated 2.5 billion rupiah (about USD 190,000).
Last year, the reclusive, gentle mammal received the highest level of protection against illegal trade at a global conference in South Africa.
More From This Section
Sinaga said the detained men, both 43, were suspected of being small players in a larger syndicate. They could face up to five years in jail and a fine of 100 million rupiah if found guilty of breaking wildlife protection laws.
"They claimed the pangolins would be shipped to Malaysia," said Sinaga, adding the scales could have been intended for use in the production of crystal methamphetamine.
It was just the latest case of pangolins being seized from alleged smugglers in Indonesia - in August last year authorities found more than 650 pangolins hidden in freezers on the main island of Java and arrested a suspect.
Protection group the International Union for Conservation of Nature classifies the pangolins found in Indonesia as critically endangered.
Pangolins, which have bad vision but a good sense of smell and hearing, are covered in tough, overlapping scales, and eat ants using pink, sticky tongues almost as long as their bodies.