The Australian Services Union has complained that Qantas is using $1,500 fortnightly jobkeeper payments to pay workers’ penalty rates.

Qantas insists the wage subsidy can be lawfully used to pay penalty rates, but unions argue the move increases the benefit of the federal wage subsidy captured by the airline.

Linda White, ASU assistant national secretary, called on Qantas to sit down with unions and come to a “joint understanding” of how jobkeeper operates, or else the union is “considering its options” including litigation.

At Qantas, staff including cabin crew and technical crews are paid the base wage in one pay period and two weeks later are paid shift penalties and allowances, in arrears.

Qantas believes that in a fortnight an employee did not work it can nevertheless use the $1,500 fortnightly jobkeeper payment to pay for penalty rates from the preceding fortnight.

But workers represented by the ASU believe penalties should be paid separately to the minimum $1,500 payment guaranteed by the jobkeeper program.

In an email to Qantas members on Monday, the ASU New South Wales secretary, Natalie Lang, claimed the jobkeeper legislation “does not support the approach that Qantas has apparently taken in relation to penalties”.

“Quite apart from the legal issues, it’s just appalling that Qantas would use taxpayers’ money to exploit its dedicated workforce in such a … disrespectful way,” she said.

“People are stressed about this and fairly questioning what exactly the advantage of working shift work is if there is no incentive for doing so.”

Lang noted Qantas has already benefited from $715m in waived fees and charges and a government promise to subsidise flights between capital cities, arguing taxpayer assistance “must be tied to properly and fairly remunerating the Qantas workforce”.

A Qantas spokesman told Guardian Australia the jobkeeper payment “is a wage subsidy for businesses affected by the coronavirus to cover the costs of their employees’ wages”.

“Employee payments are subsidised by up to $1,500 from the government each fortnight whether they are still working, on annual leave, receiving allowances or penalty rates,” he said.

“We have fast-tracked the payments for our employees even before the government has started paying the subsidy to businesses.”

White told Guardian Australia that many Qantas workers are “dealing with unemployment or underemployment for the first time in their life”.

“They’re struggling to cope and they don’t need jobkeeper to be added as another stressor,” she said.

The disquiet of Qantas’s move comes as unions are already concerned about the practice of using the jobseeker payment to pay off leave entitlements.

Earlier in April, Guardian Australia revealed jobkeeper can be used to pay leave entitlements, a “loophole” which Labor’s shadow industrial relations minister, Tony Burke, warned could mean millions of workers are left without annual leave. Qantas has already confirmed it will use jobkeeper to pay down leave.

The industrial relations minister, Christian Porter, amended draft legislation so employees must retain at least two weeks annual leave, but defended the employer practice.

Porter said the jobkeeper scheme helps “the employee stay engaged to their employer [and helps] the employer pay their employee”.

“Whether someone is at work doing limited hours because there’s very little business left at the work, or whether they’ve taken leave, what the government has said is we’re going to save that business and help that employee by subsidising their wage – whether that’s diminished hours at work or on leave with a $1,500 payment,” he said.

On Tuesday Scott Morrison was asked about the potential for exploitation of employees, either by employers threatening to sack them if they asked for the jobkeeper payment or unreasonable directions to work to earn the $750 weekly payment.

Morrison said he would be “concerned about any behaviour by employers that was coercive” and suggested a threat could be referred to regulators such as the Fair Work Commission or Ombudsman.

Morrison said employers were entitled to direct employees to work to do $750 of work a week at their regular rate of pay.

“That’s what the Act provides for,” he told reporters in Canberra. “That is not an unreasonable request that someone would work the hours that they are being paid for, that is being paid by the employer but obviously that is being met by the commonwealth through the JobKeeper program.”