The organisations which control Australia's air traffic are facing a funding black hole, with flights grounded across Australia due to the coronavirus.
Airservices Australia and the Civil Aviation Safety Authority or CASA provide provide aviation safety, regulation, air traffic control, navigation and communication, aeronautical data and airport rescue and firefighting services to airports around Australia.
Both are largely funded by the aviation fuel excise levy and other duties normally paid for by airlines.
However the organisations face a $750 million funding shortfall this year, as the aviation industry has ground to a halt due to COVID-19 restrictions.
Professionals Australia ACT director Dale Beasley said as government organisations, staff could not access JobKeeper payments.
He warned management faced tough decisions about how to continue delivering services.
"Airservices and CASA rely on this funding to employ thousands of highly trained professionals who are invaluable to the safe and efficient operation of Australia's aviation sector," Mr Beasley said.
"These agencies don't have the ability to scale operations up and down in line with the operations of industry. If an airport is open it requires the services of these professionals regardless of whether it sees five flights per day or five hundred."
While the government provided the agencies with a $250 million lifeline, they had operating costs of $1 billion per year.
Mr Beasley said without further federal government funding, thousands of jobs were under threat.
"Airservices currently has around 4400 employees. Potential job losses are difficult to forecast due to the funding models and uncertainty on when state and international borders will reopen. But in the absence of any figures from government, we're left to assume that a worst case scenario could see the agency need to match the reduction in demand forecast by industry of 39 per cent," Mr Beasley said
"They've so far avoided standing staff down, but that remains a very real possibility as there's no guarantee of future funding from government.
If an airport is open it requires the services of these professionals regardless of whether it sees five flights per day or five hundred.Dale Beasley, Professionals Australia
"Airservices have told our members that their operating environment will look uncertain for the foreseeable future. With uncertainly around the future of their employment, they're deeply concerned about how they'll support their families.
"These are highly skilled aviation sector professionals. Engineers, scientists, ICT and air safety regulators. They are not easily replaced and people we can't afford to let walk away from the industry."
The union has twice tried to meet with Infrastructure and Regional Development Minister Michael McCormack.
A spokesman for Mr McCormack said, "we will seek to maintain staffing levels over this period".
"The Australian government has a strong record on aviation safety and will ensure these agencies are appropriately funded over the 2020-21 financial yea," he said.
The aviation industry faces a slow recovery, with no end to coronavirus-related border closures in sight.
Virgin Australia's administrators this week wrote to the government, urging them to extend JobKeeper for the sector for six months.
A Labor motion that would have extended JobKeeper to thousands of airline catering workers was due to be voted on late Wednesday but pulled from the program at the last minute.
Clarification: An earlier version of this story said the Labor motion was voted down. In fact it was a motion on universities that was voted down.