Australian Border Force (ABF) staff have delivered a scathing assessment of their senior leaders, internal data obtained by the ABC has revealed.

Former commissioner Roman Quaedvlieg was sacked last week for helping his girlfriend get a job with the agency.

Just weeks before Mr Quaedvlieg took paid leave in May 2017, amid investigations into his conduct, staff recorded their views in a confidential survey.

The results, obtained by the ABC under Freedom of Information laws, paint a picture of sluggish progress in fixing cultural issues and frustration at stagnant wages.

The survey showed staff had several issues with those at the highest levels of the agency:

Fewer than one in three said senior staff set a clear, strategic direction

Fewer than one in three said senior staff set a clear, strategic direction A quarter said senior executives were of a high quality

A quarter said senior executives were of a high quality Only 22 per cent said their communication was effective

The public sector union said the results were "striking, but no surprise to us".

"Frankly, the place is a mess," union secretary Nadine Flood said.

Survey doesn't reflect workforce ability: management

Mr Quaedvlieg was the inaugural commissioner after the former customs department was combined with parts of the immigration department in 2015.

Before being jettisoned over several breaches, Mr Quaedvlieg earned $600,000 a year.

ABF strongly denied that its workforce problems, reflected in the survey results, had weakened its ability to protect Australians from unwanted drugs, weapons and people.

"Yes, we've had engagement issues with our staff," Acting Border Force Commissioner Michael Outram told the ABC.

"[But] if you look at our operational results, over the recent period of time, we're just achieving record targets and record results."

Since becoming Acting Commissioner, Mr Outram said he had forced senior executives to meet more frequently with frontline staff.

Forty per cent of ABF workers said they were satisfied with the recognition they received.

One in three think they are paid fairly

The survey also found one in three staff thought they were paid fairly for their work — a further dramatic fall in satisfaction with pay levels.

Home Affairs staff, including those in the ABF, have not received a pay rise since 2013, amid a bitter dispute between the department and the union that is now before the Fair Work Commission.

"What government has done to [immigration department] and Border Force staff is frankly grotesque," Ms Flood said.

Acting Commissioner Outram said there was "no question" the pay row had affected staff, but insisted it had not compromised operations.

"I very much hope that is resolved as soon as possible so we can move on," he said.

Results are not surprising: security expert

Completed in early May 2017 by about half the ABF's workforce, the reviews given to lower-level managers were more upbeat.

Seven in 10 employees said their supervisor cared about their health and wellbeing, and 60 per cent said their direct manager encouraged them.

Nearly all staff said they were confident they would know how to deal with corruption.

Scores from ABF staff were lower than from other immigration department staff across most survey questions.

Australian Strategic Policy Institute border security expert John Coyne said the creation of the ABF involved huge changes, and the results were not surprising.

"We're seeing an organisation that is in a massive state of flux and change, it's two years into an eight-year change program, and they're the results we'd expect to see at the moment," Dr Coyne said.

"The key performance indicators are being achieved and excelled at, so what we really need to do here is build the morale of that organisation."

The staff census is conducted across the public service annually, and since 2014, the immigration department's results have been among the worst.