Airservices Australia has continued to shed staff amid a wholesale restructure designed to offset an expected loss of $13.6 million this year.
Staff at the government-owned corporation were told of further cuts to middle management late last week and public servants told Fairfax Media an additional 180 jobs could go.
Airservices Australia would not confirm the scale of the cuts but a spokeswoman warned they would "significantly reduce the number of senior and middle managers".
Last month, unions raised concerns that up to 60 jobs were lost in the first round of cuts, which were designed to claw back $100 million from the corporation's cost base in coming years.
But on Tuesday, union officials warned the number of job cuts could be as high as 600 nationally, or 15 per cent of the workforce.
Internal briefings from chief executive Jason Harfield to his senior leadership team revealed profitability fell by 90 per cent from $45.5 million in 2013 to $4.5 million in 2015.
The briefing outlined a plan to align pay with performance, eliminate the duplication of certain functions, break "a silo mentality" and use automation to improve office productivity.
Most job losses would come from the corporate division rather than from air safety and aviation rescue fire-fighting roles.
Staff told Fairfax Media the restructure had caused uncertainty and distrust within the workforce and some were lacking motivation for daily duties.
Others criticised a lack of consultation about the scale of job cuts and senior leadership being unable to provide clarity on changes.
Mr Harfield wrote to staff earlier this year to insist he would not know the full impact of job losses until a wholesale review of operations progressed.
"Be assured that we are working as quickly as possible to resolve uncertainty in a fair, responsible and considerate way," he said.
Last month, an Airservices Australia spokeswoman said the corporation was working closely with unions and consulting with staff during an uncertain time.
"While we have already made some progress on our broader transformation agenda, we are not moving fast enough," she said. "We need to be more collaborative, less complex and better enabled to change."
Professional Australia campaign director Matt Harris, whose union represents public servants at Airservices Australia, said it was "not a great place to work at the moment".
The restructure comes before the implementation of the $1.5 billion OneSKY program, which will combine civilian and military navigation systems by 2021.
Airservices Australia employs more than 4400 staff and manages 11 per cent of the world's airspace. It has 29 towers and 1000 air traffic controllers around the country. Last year it managed the movement of 4.5 million flights carrying 90 million passengers.
The network is co-ordinated from the national operations centre in Canberra where 15 to 20 staff try to smooth the passage of about 11,500 flights a day, working to minimise the risk of collisions, while allowing the maximum number of aircraft to fly safely in our skies.