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Qatar Airways has been flying near-empty, and sometimes entirely empty large passenger jets every day between Melbourne and Adelaide to exploit a loophole allowing it to run extra flights to Australia.

Qatar’s ghost flights – an open secret within the aviation sector – are “taking the piss” out of Australia’s strict aviation laws, industry sources say, and are occurring despite the Albanese government rejecting the airline’s formal request to increase flights out of concern the extra capacity would go against Australia’s “national interest”.

The Qatari-government owned airline is currently limited to running 28 weekly services into Australia’s four major airports – Melbourne, Sydney, Brisbane and Perth – allowing it to run once daily return flights from Doha into each of these cities.

However under the existing bilateral agreement, there is no limit placed on how many services Qatar is able to run to non-major airports.

In November 2022, Qatar Airways introduced a second daily, non-stop flight between Doha and Melbourne, but with Adelaide registered as its destination and departure port in Australia.

By flying the 354-seater Boeing 777-300ers between Melbourne and Adelaide, it means the airline does not exceed the 28 weekly services into major airports it is allowed to operate under the existing bilateral agreement.

However, the airline is not permitted to sell tickets on the leg between Melbourne and Adelaide to domestic passengers under Australia’s aviation laws. It can only carry the few international passengers booked through to Doha who have chosen the two-legged route instead of the separate daily non-stop flight between Adelaide and Doha that Qatar Airways also operates.

Qatar’s QR988 arrives from Doha into Melbourne at 11.30pm each night, where almost all passengers disembark. However, any passengers booked to stay on the plane for the Adelaide leg must endure a six-hour layover in Tullamarine airport’s international terminal before the flight departs at 5.35am, because of Adelaide airport’s 11pm to 6am curfew.

The QR989, which flies the outbound direction to Doha, departs Adelaide at 11.40am each day, lands in Melbourne 1hr 30min later, and travellers have a shorter 1hr 45min layover in the international terminal before the majority of passengers board for the non-stop flight to Doha.

Passenger numbers on the 354-seat aircraft average in the single digits on the inbound QR988 leg from Melbourne to Adelaide with the overnight layover, according to Guardian analysis of government flight data and confirmed by sources with knowledge of the flights. This flight sometimes carries no passengers at all.

The outbound QR989 Adelaide to Melbourne service has proved slightly more popular with travellers to Adelaide – there are between 20 and 35 passengers on this flight on average, according to the analysis.

Patronage is so low on both Melbourne-Adelaide legs of these trips they are considered ghost flights – the term for a usually loss-making service operated with zero passengers or fewer than 10% capacity in order to meet an obligation.

The separate, non-stop flight between Doha and Adelaide that Qatar Airways flies as part of its Auckland-Doha service is a significantly more popular option with Adelaide travellers, the government data shows.

Qatar Airways previously ran a second daily service between Doha and Sydney by extending the final port to Canberra, exploiting the same legal option.

While flights with a secondary port can encourage global airlines to better serve smaller cities in Australia, the scheduling of QR988 and QR989 have led to a view within the aviation sector that they are primarily functioning as second daily Melbourne services, multiple sources said.

Such was the case that when Qatar Airways launched the flights in November, it was not selling tickets on the Melbourne-Adelaide legs to international passengers for the initial weeks of the service. The overnight layover was originally more than 11 hours.

Frustrated by Qatar exploiting the loophole, the department of infrastructure and transport placed a condition on the timetable approval “for these flights on this route that they must be available for sale for passengers and cargo arriving and departing from Adelaide”, a spokesperson for transport minister Catherine King said.

The department now continuously monitors Qatar Airways sales to ensure “this condition is being met by the airline”, the spokesperson said.

An industry source said: “The whole purpose is to get to Melbourne … I mean they weren’t even selling tickets (to Adelaide) for the first few weeks.”

“They were taking the piss out of the industry and the laws,” the source said.

The extra flights will be allowed to continue even after the Albanese government rejected Qatar Airways’ push to fly an additional 21 services into major airports – something supported by most in the aviation and tourism industries as well as state premiers – after “taking into account all national interest considerations”.

The Guardian understands foreign policy factors influenced the decision. Others including Australian women suing Qatar Airways for damages over forced invasive bodily examinations, and Qantas, were opposed to the greater air rights for the airline.

The rejection has fuelled claims that refusing Qatar additional air rights benefits Qantas, as it and other global airlines remain constrained from increasing international flight capacity to Australia, at a time of stubbornly high air fares and record operator profits.

Qatar Airways declined to comment.