The crystal meth or 'ice' reportedly has a street value of Rs. 8 crore.
Methamphetamine is used as a recreational drug for its euphoric and stimulant properties.
Deputy finance minister Benja Louicharoen said customs officials became suspicious after x-raying the duo's luggage.
A search revealed a total of 12 kilos of drugs in hidden compartments in their bags.
The two men reportedly confessed it was their second trip to Thailand, the Bangkok Post reported.
The first had been to check out the smuggling route.
After they arrived in Samui, they were told, there would be someone waiting to collect the drugs and take them to Bangkok.
The men will be charged and if convicted could even face the death sentence.