The Australian passenger on the flight from Brisbane acted aggressively and began pounding on the cockpit door before he was handcuffed by the crew, Heru Sudjatmiko, airport manager for Virgin Australia, told Metro TV.
"There was no hijacking at all," he said. "It was only a miscommunication."
The passenger was arrested for creating a disturbance, he said.
The Boeing 737 was carrying more than 130 people on the flight to Bali, which is a leading tourist destination for Australians.
"The aircraft landed safely and at no point was the safety of passengers in question," an airline spokeswoman said in Australia.