Qantas says the Boeing 737 with the flight number QF50 that made an emergency landing at Sydney Airport on Wednesday was not really a Qantas flight at all.

The plane was flown by wholly owned, New Zealand-based Qantas subsidiary Jetconnect.

The pilots union and the ACTU are citing the emergency landing, triggered by a faulty fuel transfer valve causing a false alarm, as proof that Qantas is operating Jetconnect as a sham company to lower pilots' wages and conditions.

When QF50 took off from Auckland Airport in the early hours of Wednesday morning, passengers would have been forgiven for thinking they were flying with Qantas.

The pilot and flight attendants wore Qantas uniforms and the passengers ate Qantas food.

Indeed, when the ABC reported the emergency landing that morning it was Qantas fielding media inquiries about the incident.

"Well, it's marketed as Qantas, the aircraft are painted in Qantas livery, Qantas is written down the side of the airplane, in fact it says 'The Spirit of Australia'," Pilots Association spokesman Adam Susz said.

"On the other hand you've got a New Zealand flag and a New Zealand-registered aircraft, so it's quite a contradiction."

It is that contradiction - was QF50 a Qantas or a Jetconnect service - which is at the heart of the dispute that was heard before Fair Work Australia this week.

The Pilots Association says QF50 shows that Jetconnect, which was formed by Qantas in 2001 to fly the trans-Tasman route, was created solely so pilots could be employed under lower New Zealand awards.

"What's been clearly identified during the case is that it's basically a sham arrangement. It really is Qantas by another name," Mr Susz said.

"It's a company that's controlled by Qantas, managed by Qantas and governed by Qantas. In fact, I don't think they even have a bank account in New Zealand.

"Really it's just an industrial set-up to avoid paying Australian terms and conditions."

The ACTU also made submissions before Fair Work Australia in the case, arguing that if Qantas succeeded in sending jobs offshore with Jetconnect, it would set a dangerous precedent for other industries.

"We're arguing that Jetconnect is not a real airline. It has no claims, it has no customers, it has no real assets. I mean, it doesn't even have a bank account in it's so-called home country New Zealand," ACTU president Ged Kearney said.

"It is a subsidiary wholly owned, controlled and operated by Qantas. It is a shell company, in other words."

Ms Kearney also criticised Qantas's response that it has not made one pilot redundant in the past 40 years.

"That's a nonsense argument because jobs are about jobs that are potential, that are real, that are future jobs. It's not just about jobs in the past," she said.

"They are simply not employing Australians under Australian terms and conditions.

"They are employing people overseas, offshore, in sham companies so they can avoid paying Australian wages and conditions, they can avoid being a good corporate citizen and giving back to the very communities and countries that actually have loved Qantas and used Qantas very loyally over the last 40 years.

"It's really an appalling situation and an appalling behaviour by a large iconic company."

Qantas declined to comment to PM, but in a written statement said Jetconnect was a New Zealand-registered company, operating New Zealand-registered aircraft.