About 2,500 Qantas and Jetstar employees will be stood down for two months because of domestic coronavirus border closures, in a move unions have criticised for being taken one day after the announcement of a government wage support package. Domestic pilots, cabin crew and airport workers will be stood down, mostly in New South Wales, but won’t lose their jobs. The Qantas chief executive, Alan Joyce, expects borders to be closed for at least two more months due to the knock-on effects of greater Sydney’s ongoing Covid-19 crisis and lockdown. Employees being stood down will be given two weeks notice and be paid until mid-August. The announcement comes a day after the Morrison government unveiled a $100m program to help domestic airlines retain their staff through lockdowns and border closures. The government scheme allows domestic airlines to claim $750 a week for half of their aircrew workforce if they can show a 30% downturn in business since Sydney was declared a national hotspot and could not retrench workers. Joyce said the different schemes meant that the stood down Qantas workers, which include 2,500 in domestic operations and 6,000 in international operations, will be receiving different levels of support from either Covid disaster payments or the new scheme. He said engineers would not be stood down as they are needed for plane maintenance, but acknowledged that outsourced ground workers would not be eligible for the payments – days after the federal court found against the legality of Qantas outsourcing. Sign up to receive an email with the top stories from Guardian Australia every morning “This is clearly the last thing we want to do, but we’re now faced with an extended period of reduced flying and that means no work for a number of our people,” Joyce said on Tuesday. Qantas had “absorbed a significant amount of cost” as a result of the lockdowns by continuing to pay staff their full rosters despite cancelled flights, he said. “Fortunately, we know that once borders do reopen, travel is at the top of people’s list and flying tends to come back quickly, so we can get our employees back to work.” At a press conference later on Tuesday morning, Joyce defended standing down the staff in light of the significant government support it has received throughout the pandemic, which is on track to reach $2bn. Joyce said the way government support had been reported was “misleading”, and explained the majority had been from jobkeeper payments, repatriation flights and ongoing freight – services which he said “benefit the economy”. He reiterated that the airline was still working on its vaccination pass and its intention to offer frequent flyer points and prizes as incentives for customers to get vaccinated. But Joyce acknowledged it was no guarantee that its international flights would resume by the December timeframe it has set. Unions are furious at the Qantas decision. In a tweet, the Transport Workers’ Union said the timing of the government’s wage subsidy and the Qantas announcement on Tuesday meant the package had been “tailored” for the airline. “This is the Republic of Qantas,” the union said. Qantas had gone from operating at nearly 100% of its usual domestic flights in May to less than 40% in July. This time last year, more than 20,000 employees were stood down.