The load of an estimated 1.3 tons was worth around 2.07 trillion rupiah ($116.2 million), he said. Authorities were still searching the boat to see if there was more.
Ketamine functions primarily as a fast-acting anesthetic but is widely abused as an illicit party drug. Its distribution is tightly controlled and monitored in Indonesia.
State news agency Antara reported that the vessel was registered under a Tanzanian flag and that it was intercepted in waters around the Riau Islands province near Singapore.
Eight crew aboard the vessel — seven Myanmar nationals and a Taiwanese — have been detained, the narcotics agency said.
"We are still investigating with regards to the origin of the load, port destination, who was the sender and who was the receiver," Suyudi said.
Indonesian authorities seized 3.37 metric tons of cannabis buds last month when they foiled a smuggling attempt from Thailand, arresting 12 suspects.
In 2021, Indonesian police busted a smuggling ring that moved 2.5 tons of methamphetamine into the country from Afghanistan, with 17 suspects arrested.
Indonesia has some of the world's toughest anti-drug laws, including the death penalty for traffickers, but has maintained a moratorium on executions for several years.