Authorities in Papua province said they seized 2,227 of the palm-sized turtles which were stuffed into boxes on a boat docked, in the remote town of Agats, AFP reported.
"Officers saw a port worker carrying three big boxes and got suspicious," Papua police spokesman, Ahmad Musthofa Kamal, said late Thursday.
"This is a protected species and they are not for sale."
Following the discovery, police arrested another man believed to be involved in the trafficking bid. The port worker was not detained.
If convicted, the arrested man could face up to five years in prison and a 100 million rupiah ($7,000) fine, police said.
It was not clear where the turtle shipment was headed