Senior customs official Zulkurnain Mohamed Yusof said agents found 5,255 baby red-ear slider turtles kept in small baskets in the luggage of two Indian nationals who flew in from Guangzhou, China, on June 20.
The men are expected to be charged and could face up to five years in jail and a fine, he said.
The red-ear slider is one of the world’s most commonly traded turtles meant for the pet and meat markets.
Permits are required as young turtles are susceptible to carrying salmonella and pose health concerns.
Mr Zulkarnain said officials also found 14.34kg of methamphetamine worth 717,000 ringgit (£136,000), hidden in special compartments in boxes that were hand-carried by two men.
One of them flew in from Hyderabad, India, on June 19 and another on June 20 from Bengaluru, he said.
The two men, believed to be drug mules, are expected to be charged and face the death penalty if convicted.