Lion Air's slogan "We make you fly" came a bit too close to home when one of the Indonesian airline's pilots tested positive for crystal meth after being arrested only hours before he was due to take off.

The 44-year-old pilot for Indonesia's largest domestic airline by passenger volume was arrested in a hotel on Saturday in Surabaya, Indonesia's second city, a spokesman for the National Narcotics Agency said yesterday.

The pilot was due to fly to Makassar, on Sulawesi island; Balikpapan, on Borneo; and back to Surabaya, the spokesman said.

"The pilot ... was arrested [on Saturday] with 0.04g of crystal meth slipped in an envelope and he later tested positive for the drug," he said.

He is the second Lion Air pilot to test positive this year.

Crystal meth is known as shabu-shabu in Indonesia.

Between 2010 and 2011 it overtook dagga as the No 1 drug in the country of 240million people, a senior narcotics agency official said.

Budget airline Lion Air serves domestic routes and also plies between Indonesian cities and Singapore, Kuala Lumpur and Ho Chi Minh City. It could not immediately be reached for comment.

The government will now require pilots and cabin crew to undergo drug and alcohol tests before boarding a plane, a transport ministry spokesman said.

Indonesia is struggling to upgrade its civil air safety after a series of deadly accidents that led the European Union in 2007 to ban all Indonesian airlines from its airspace.

The ban was lifted progressively, starting in 2009.