The Department of Transport in Indonesia has accused Tigerair Australia of breaching its licence conditions after a snap decision to suspend the budget airline from flying from Bali to Perth, Adelaide and Melbourne.

Hundreds of passengers were left stranded after the airline was sanctioned in Bali for allegedly breaching Indonesian regulations.

In a lengthy statement issued on Wednesday evening, a spokesman for the Director General of Air Transport in Indonesia accused the budget airline of breaching its licence. The accusations appear to revolve largely around ticketing arrangements.

The statement indicated the budget airline operates charter flights and should not be issuing one-way tickets.

It said ticketing should be controlled by the airline's parent company Virgin Australia.

The statement issued by the head of public relations at Air Transport, Agoes Soebagio, said all foreign airlines must comply with the Indonesian regulations.

"We will not hesitate to give sanctions and suspend the operation of foreign airlines which violate the flight regulations in Indonesia," it said.

Indonesian aviation expert Gerry Soejatman told the ABC Tigerair Australia either knew it was breaching the rules or had been given bad advice.

"This isn't the first abuse of charter flights into Bali by a foreign airline," Mr Soejatman said

"Tigerair's claim that this is a new requirement by the Indonesian regulator is laughable."