Jakarta airport official Salahudin Rafi says the two Kuwaitis were about to enter the departure area Friday when X-rays showed their bags were filled with sedated snakes.
The men told investigators they planned to sell the pythons to collectors in the United Arab Emirates.
Rafi says the men are still being questioned. If charged with attempting to carry wild animals on board the Emirates plane, they could face up to seven years in jail and a fine of $32,000.
In December, police at Abu Dhabi's airport stopped a passenger who passed through an Indonesian airport carrying a box containing four snakes, two parrots and a squirrel.