A Thai national and four Myanmar nationals were found aboard the vessel, Indonesian Navy spokesperson Commodore I Made Wira Hady Arsanta Wardhana said.
Officers apprehended the ship after it turned off its lights and increased its speed to try to flee Indonesian waters in the Tanjung Balai Karimun region, Riau Islands, according to the navy.
Officers seized nearly 100 yellow and white sacks holding about 1.2 tonnes of cocaine and 705 kilograms of methamphetamine worth 7 trillion IDR, among the largest busts in the Southeast Asia's largest economy.
Indonesia has among the world's strictest anti-narcotics laws and drug trafficking is punishable by death.
The navy said the ship, bearing a Thai flag, was taken to a navy base in Tanjung Balai Karimun. It did not give details of the crew members' origins apart from their nationalities.
Officials are still investigating where the drugs came from and where the ship was heading.