Mr Heru said the man was handcuffed and put into a rear seat of the Boeing 737-800.
Hijacking reports were "clearly a miscommunication'', and the pilot had sent a distress call and told air traffic control that the plane was hijacked.
"I don't know why that happened.''
ABC News reported Palani Mohan, who was on a Garuda Indonesia flight taking off from Bali, as saying military-style trucks had rushed towards the plane.
"The captain of my plane made an announcement saying we were delayed indefinitely because a hijack was going on in Bali airport, about 150 metres away from us.
"I saw at least five vehicles including military-style trucks, filled with men in uniform, rushing towards the plane.
"Bali airport seems to be in lockdown, we've been told no planes will be departing or arriving.''
Virgin later issued a statement saying that all 137 passengers and 7 crew had disembarked the aircraft.
"There was a disruptive passenger on board and the pilot notified authorities in advance of landing, as per standard operating procedures,'' the statement said.
"The passenger was unarmed and is now in the custody of the Indonesian authorities.''
Do you know anyone on Virgin Flight VA41? Email Newsdesk@nzherald.co.nz