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Unions have won a landmark federal court case over jobkeeper against airline Qantas, with the federal court ruling companies have to pass the full wages subsidy on to workers.

If Qantas does not successfully appeal it will be required to make backpay to hundreds of workers, each of which unions estimate could be due thousands of dollars.

Other companies across the economy could also be forced to make similar payments.

A group of unions, including the Transport Workers Union and the Australian Services Union, publicly accused Qantas of manipulating shifts to avoid paying workers anything on top of the $1,500 a fortnight jobkeeper payment.

But while the unions accused Qantas of wage theft, allegations that Qantas deliberately manipulated rosters for company gain at the expense of workers or taxpayers were not put before the court.

During the legal proceedings, Qantas argued that payments made during a fortnight for work done previously should count against jobkeeper payments.

But on Thursday judge Geoffrey Flick found that the jobkeeper law “means what it says” and refers “only to the monies an employee is contractually due to receive during any given fortnight for work performed during that same fortnight”.

“If the consequence of the interpretation now given … is that idiosyncrasies arise in respect to the quantification of amounts that an employee is to receive – including the prospect that employees may benefit from a “windfall” – so be it,” he said.

“It remains a matter for the legislature to “tweak” or adjust the scheme if it sees fit.”

He said the ruling potentially affected all employers and workers receiving jobkeeper.