The accident on Monday occurred at a military airport that also handles civilian flights to ease congestion at Jakarta's main commercial airport.
Batik Air said in a statement that its plane carrying 49 passengers and seven crew was "touched" while taxiing for takeoff by a TransNusa aircraft that was being towed.
Images posted online showed severe damage to the wing of the Batik Air jet, a Boeing 737-800.
The airline said passengers and crew were safely evacuated.
TV images showed the wing of the Batik Air aircraft in flames as fire trucks and ambulances gathered on the runway.
Watch the video: