A bomb squad rushed to Juanda International Airport in Surabaya city after the threat said flights from there to the capital, Jakarta, had been targeted.
Ervan said a plastic bag with liquid materials used to make explosives was found in the passenger lounge.
Garuda postponed one flight but service returned to normal later Wednesday.
Indonesia, the world's most populous Muslim nation, has been hit by a string of terror attacks blamed on al-Qaida-linked militants that have killed more than 260 people since 2002.
