In a majority decision on Friday, the Full Court of the Federal Court dismissed an appeal brought by the three unions seeking to have payments made to workers, including a man battling cancer and another with heart disease.

Justices Craig Colvin and Steven Rares said a stood-down employee is not required to present for work and therefore cannot be said to take leave or be absent.

The unions hadn't challenged the stand-down decision and instead claimed employees who had been stood down had the right to take paid personal care leave and compassionate leave without deduction, they said.

"In our view, the agreement provides for no qualification of that kind to the provision that entitles deduction of payment for any day when the employee has been stood down," the judges said.

The dissenting judge, Justice Mordecai "Mordy" Bromberg, said the primary judge had erred.

While acknowledging the orders in the terms the unions sought was not appropriate, he said a declaration should be made to the effect that for workers entitled to sick leave, Qantas was not authorised to withhold the payment.

The Australian Council of Trade Unions said Qantas had abandoned long-term workers with serious medical issues by refusing to allow access to sick leave during a stand-down

"They have a responsibility to these workers, some of whom are dealing with life-threatening medical issues, and have the money to pay out sick leave. They are refusing to do so," ACTU secretary Sally McManus said in a statement.

"These workers are uniquely disadvantaged, being stood down and also unable to pursue work elsewhere due to illness."

The Transport Workers Union said sick workers had been devastated by being unable to use entitlements built up over years.

"These workers have worked hard over many years, they have built up leave and when they fell sick Qantas has told them they are on their own," TWU national secretary Michael Kaine said in a statement.

A Qantas spokesman said COVID-19 and border restrictions meant the majority of their employees have had no work for months.

"The company has taken on more than $2 billion in debt as revenue has collapsed. It's been an incredibly difficult time for everyone," he said.

"We understand that some employees will be disappointed today, but there's now been two courts who have confirmed that employees who are stood down are not eligible to receive paid sick leave because there is no work to be absent from. This is not just true of Qantas, but across the economy.

"Our employees, whether they were working before COVID or on sick leave, have access to JobKeeper, annual leave and long service leave while they are stood down, and are being provided other support."

Australian Associated Press