Tigerair will be allowed to fly stranded Australian passengers home from Bali, but the future for the budget airline’s foray into Indonesia remains unclear.

The low-cost carrier suspended all flights in and out of Bali earlier this week, after allegedly breaching the Indonesian government’s aviation regulations relating to its licensing conditions.

Tigerair says it has now been granted permission to operate flights from Bali to Australia until Monday, in order to get thousands of stranded passengers back home.

A Boeing 737-800 aircraft will fly empty to Bali to collect what the airline says is around 2000 passengers, and return them to Australia.

However, the airline has cancelled all flights from Australia to Bali until next Friday, January 20.

“Flights Australia to Bali from Saturday 21 January onwards are under review,” the airline said in a statement.

“Tigerair sincerely apologises to its customers for any inconvenience caused.”

Some passengers may remain stranded

A spokeswoman told the ABC flights from January 17 onwards, out of Bali, were also under review, leaving passengers already in Bali, but booked on flights out past January 16, facing uncertainty about how they will get home.

Many ticketholders have told the ABC they face thousands of dollars of out of pocket expenses, over accommodation bookings and flights on alternative carriers.

Virgin Australia has put on additional flights to get people home.

Virgin acquired Tigerair in 2014 for a nominal $1, as the airline grappled with losses since its introduction to the market in 2007.

The airline initially refused to say why it had been forced to ground its fleet flying to Bali, saying it was a “decision by the Indonesian government to impose new administrative requirements” for the operation of its flights.

A spokeswoman for the airline told the ABC on Wednesday they could not say what those requirements were, “because we don’t want to pre-empt the process or adversely affect the outcome”.

However, the department of transport in Indonesia has accused Tigerair Australia of breaching its licensing arrangements.

A statement from the department indicated the budget airline operates charter flights, and should not be issuing one-way tickets.

Tigerair said it was exploring a number of options to continue its operations to Bali, including agreeing to new conditions with the Indonesian Government and using Tigerair’s existing Airbus A320 fleet to operate Bali flights, pending regulatory approval.