The federal organisation that provides air navigation services has paused recruiting and cut spending on staff travel and contractors to reduce costs as COVID-19 hits its finances.
Airservices Australia, which relies on airline activity for much of its revenue, has also told more than 80 staff to use "excess" annual leave, and asked others to reduce their balances.
While much of the federal public sector has so far escaped financial damage from COVID-19, Airservices Australia faces a hit to its revenue from airlines because of the disruption to the aviation industry.
Amid union calls to support the organisation, the government said on Tuesday it would keep Airservices Australia appropriately funded.
Airservices Australia this month told a parliamentary committee investigating the government's response to COVID-19 that the organisation had paused recruitment, and cut spending on overtime, staff training, consultancies and contractors.
It directed 82 staff who had accrued more than 18 months' worth of annual leave to reduce their balances.
An Airservices Australia spokesperson said the organisation had also asked other staff to take leave during the pandemic and the majority had met the request.
A spokesman for a union representing Airservices Australia staff said employees were sharing the uncertainty COVID-19 had brought to the aviation industry.
Professionals Australia's ACT and Australian government group director Dale Beasley said unlike other public sector agencies, Airservices received almost all its funding from industry activity.
The aviation downturn had gutted Airservices Australia's funding, but the organisation couldn't scale operations up and down in line with industry, Mr Beasley said.
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"If an airport is open it requires the services of these professionals regardless of whether it sees five flights per day or 500," he said.
"This saw a lot of pressure build up, as staff and managers grapple with funding challenges not being faced in other agencies.
"The agency's engineers and professionals whom we represent have been pragmatic, adapting to challenging ways of working and also reducing their leave balances to help manage the funding shortfalls.
"But ultimately, it shouldn't be the responsibility of staff to fund the operations of the agency.
"The aviation industry and Airservices are the key enabler to so much of the Australian economy. We need to see more action from government to ensure Airservices and the key players in industry are able to ramp back up and aid in the COVID recovery."
A spokesperson for Deputy Prime Minister and Transport Minister Michael McCormack said the government would keep both Airservices Australia, and the Civil Aviation Safety Authority, appropriately funded over the 2020-21 financial year.
He said the funding would let the organisations maintain necessary staffing levels "and provide the level of service expected by the flying public".
Airservices Australia's spokesperson said none of its responses to COVID-19 would stop it providing safe air traffic management and aviation rescue and firefighting services.
"Airservices Australia is playing its part in assisting the aviation sector manage the COVID-19 crisis while maintaining the necessary capacity to support the re-emergence of the industry when coronavirus-related restrictions are lifted," the spokesperson said.