The 39-year-old, identified only as MS, was apprehended shortly after flying a passenger plane from Kuala Lumpur to Jakarta late on Wednesday. While the airport officials did not name the pilot's employer, the flight number indicates it was a Malaysia Airlines flight.
Customs officials said they found 14 bags of ecstasy tablets in the pilot's suitcase, plus four grams of meth in his hand luggage.
They said the pilot had transported the illicit substances at the request an unidentified person with the promise of a 50,000 ringgit ($12,240, €10,630) reward.
They also said the pilot had been under the influence of drugs while flying the jet.
"The results of his urine test came back positive for meth, MDMA and cocaine," said an official.
"What concerns all of us is that this person's profession is a pilot. At the time he arrived, he had just flown that plane from Kuala Lumpur to Indonesia."
Malaysia Airlines has declined to comment on the case while the investigation is ongoing, but said it does not tolerate form of misconduct and is currently conducting its own internal review.
"Malaysia Airlines will extend its full cooperation to the relevant authorities in accordance with all applicable laws and regulations," read a statement. ALSO READ: Cocaine vaccine: Could it help drug addicts?
Pilot could face death penalty under Indonesia anti-drug lawsAn officer with Indonesia's national drugs crime unit, Awaludin Amin, described the pilot as a courier working for an international syndicate. He also said this was not the first time that MS had smuggled drugs into Indonesia.
The country has some of the toughest anti-drug laws in the world. The drug-trafficking charges levied against MS can carry life sentences or even the death penalty — although the country has maintained a moratorium on executions for the last decade.
However, around 90 foreign alleged traffickers remain on death row, along with over 400 Indonesians.
Indonesia last carried out the death sentence in 2016, when one Indonesian and three Nigerians were convicted of drug offences and executed by firing squad.
In 2015, two Australian nationals were executed for attempting to smuggle heroin off the popular resort island of Bali as part of the "Bali Nine" drug ring.
In March this year, two British men were sentenced to nine and 11 years in prison respectively after being found guilty of smuggling cocaine onto Bali. ALSO READ: A new drug makes your blood toxic to mosquitoes
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