The 39-year-old Malaysian citizen, identified only by his initial MS, was also allegedly on duty while under the influence of narcotics, said Eko Hadi Santoso, director of narcotics crimes at the National Police Criminal Investigation Agency.
The case was uncovered late on Tuesday when customs officers inspecting baggage at the international arrival's terminal of Soekarno-Hatta Airport noticed a suspicious suitcase during an X-ray screening.
The luggage was later collected by the suspect, whom police identified as a pilot for Malaysian Airlines on flight MH727 from Kuala Lumpur to Jakarta, Santoso said.
He said customs officers took the pilot and the suitcase to a customs inspection room for further examination.
Police said they found 14 large packages containing more than 70,000 ecstasy pills, weighing a total of about 26 kilograms, along with a separate package of methamphetamine.
Police narcotics investigators took over the case.
"He has been named a suspect and detained," Santoso told a joint news conference at the airport on Friday where police showed the drugs seized from the pilot to reporters.
"Investigators are still conducting further inquiries to develop the network above him," he said.
During questioning, MS allegedly told investigators that he had been instructed by another person to transport the ecstasy to Jakarta in exchange for 50,000 Malaysian ringgit (about $A16,500), Santoso said.
The pilot was told that after arriving in Jakarta he would receive further instructions from a person believed to be in Malaysia and that the drugs would be collected from his hotel by another individual.
According to Santoso, the pilot admitted to previously transporting drugs on two occasions.
He told investigators that he had once delivered methamphetamine to Sabah, Malaysia, and later transported 7 kilograms of methamphetamine to Jakarta.
The latest shipment on Tuesday was intercepted before it could be delivered.
A drug test administered to the suspect showed positive results for methamphetamine, ecstasy and cocaine, Santoso said.
The pilot is being investigated under Indonesia's narcotics law, which carries severe penalties for trafficking large quantities of illegal drugs, including the possibility of the death penalty.
Police did not immediately say whether the suspect had legal representation.
Malaysia Airlines said it was co-operating with authorities and had launched an internal review of the incident.
"Malaysia Airlines wishes to reiterate that it does not tolerate any form of misconduct and is currently undertaking an internal review of the matter," the airline said in a statement cited by Malaysian media.
The carrier added that the safety, security and integrity of its operations remain its top priorities.
Hengky Tomuan Parlindungan Aritonga, head of the Soekarno-Hatta Airport Customs Office, said the case was unusual because the alleged smuggling operation had infiltrated the aviation industry, where crew members receive separate baggage claim tags identifying them as airline personnel, he said, which creates a distinct processing channel from that used by passengers.
"At check-in in Kuala Lumpur, the baggage followed a different channel because the claim tag identified it as crew baggage," Aritonga said.
He said investigators believe the trafficking network exploited special privileges typically granted to airline crews around the world, allowing them to move through airports under procedures different from regular passengers.
The Australian police recently arrested a Thai airline employee and charged her for allegedly importing more than 1 kilogram of heroin into Melbourne.
