Sadao customs officers find sacks of live pangolins under the bonnet of the man's car.
Footage of a pangolin was seen sitting on its tail while grasping a tree, as captured by Chester Zoo conservationists.
The haul included 1,800 boxes of frozen pangolins, 572 more frozen pangolins in six freezers, 61 live pangolins in cages, and 361kg of pangolin scales.
It says past success in seizure of smuggled wildlife was due to Sepanggar Bay port being more efficient than other ports.
The critically endangered creatures were seized in two separate raids in Kedah yesterday.
Thai Customs believe the pangolins originally came from Indonesia before they were smuggled into Malaysia and later to Thailand to be sent to Laos and China.
The forensic tests will determine if the pangolins came from Sabah or elsewhere.
It calls for timely tip-offs on tourists being fed meals from meat of pangolins, wild boar, turtles and pythons.
The illegal shipment of scales from the critically endangered pangolin have been uncovered at the Kuala Lumpur International Airport by Customs officials.
The protected species was seized following a raid by seven policemen and four wildlife department staff on a house in Taman Desa Seraya.