Staff at the Civil Aviation Safety Authority are overworked due to significant job cuts and the majority of staff lack confidence in senior leadership, the union representing professionals such as scientists and engineers, Professionals Australia, said.

The union on Wednesday lodged a submission outlining its concerns to a Senate inquiry and has called for federal government intervention to fill key positions within CASA to mitigate safety risks.

It has also called for an independent workplace review to identify issues leading to employee dissatisfaction and develop improvement strategies.

Deputy Prime Minister Michael McCormack, who is also Transport Minister, said CASA was confident it had the necessary number of qualified staff to meet safety requirements and the government had ensured the agency was appropriately funded to carry out this work.

He said the government regarded employee welfare very seriously and would consider any recommendations by the Senate committee in due course.

Professionals Australia provided two examples within the authority which highlighted the understaffing issue. The Southern Region office, which covers Melbourne, Hobart and parts of regional NSW and Victoria, has had its staff cut from 53 to 24 in the past seven years.

In Brisbane, the authority's safety systems inspectors have been reduced from six to only 1.4 full time equivalent positions.

This happened at a time when Virgin Australia, headquartered in Brisbane, went into administration, slashed jobs and sold off or stored aircraft. According to the union, due to the cuts there was no change and risk management inspector assigned to the team overseeing the airline.

Professionals Australia director of the ACT branch and Australian government group, Dale Beasley, said CASA's air safety workforce was in crisis and stretched to its limits, "increasing the very real risk of a catastrophic accident".

"[Their] stubborn refusal to replace these vacant technical air safety positions has resulted in excessive overwork, a major reduction in face to face audits and fewer field inspections and the impacts are being felt right across the country," Mr Beasley said.

"If we are going to avoid the types of disasters caused by the breakdown in aviation safety regulation, which have occurred in the places like the United States and New Zealand, then CASA must address its understaffing and workplace culture problems as a matter of urgency."

The union cited data from the APS census which showed only 39 per cent of employees believed senior management was able to communicate the direction and priorities of the agency. Only 31 per cent of staff surveyed responded positively to feeling valued by the agency and that internal communication was effective.

In calling for an independent review of the workplace culture, Mr Beasley said Australia's $43 billion aviation industry relied on the agency's staff who were being let down by senior management and a "broken" workplace culture.

"The results are a damning indictment of CASA's senior leadership and the workplace culture they have allowed to develop," he said.

Mr McCormack said some staff feedback from the census had illustrated strengths in the agency's workplace culture.

This included 72 per cent agreeing there was strong employee engagement, 77 per cent reporting they were proud to work at CASA and 78 per cent saying they experienced high levels of engagement with and confidence in direct managers.

"CASA continues to deliver the high standard of aviation safety that government, the travelling public and the broader community has come to rely on and I look forward to continuing to work closely with them to ensure Australia maintains the enviable position as a world leader in air safety," Mr McCormack said.

The Public Service Commission indicated CASA would not be participating in this year's APS census, a decision lashed by Member for Bean David Smith.

Mr Smith, formerly a director with Professionals Australia, said when he left the union in 2018 the engineering and technological workforce at the agency "was under immense pressure" and this had only become worse.

He was concerned that not participating in the census could be a way of hiding the serious issues plaguing the agency.

"It is critical that CASA has the capability to do their job and critical for the government to make sure their workforce is properly staffed," he said.