The number of public servants who say they have witnessed corruption has doubled in three years, reigniting calls for a national anti-corruption commission.

Key points: Australian Public Service Commission says cases of corruption in the bureaucracy are rare

Australian Public Service Commission says cases of corruption in the bureaucracy are rare Transparency International said it showed the need for an independent watchdog

Transparency International said it showed the need for an independent watchdog APSC said the majority of employees knew how to report corruption

A survey of the bureaucracy revealed 5 per cent of respondents said they had seen misconduct, with cronyism and nepotism the most common charge.

The Australian Public Service Commission (APSC) has admitted there is some corruption in the bureaucracy, but stressed it remained rare and staff were vigilant to the threat.

But former New South Wales Supreme Court Judge Anthony Whealy said corruption could be more widespread than many realised.

"We know that in the public service whistleblowing is absolutely frowned on," Mr Whealy told the ABC.

"People who work in the public service, in many instances, would be afraid to report their superiors or even their equals who are involved in corruption."

For the first time, the APSC has asked whether staff believed they worked in a high corruption risk environment.

A majority of respondents in 59 agencies agreed this was the case.

Mr Whealy, who is also the president of Transparency International, said it showed the need for an independent watchdog.

"I think there is a significant chance that these figures are very conservative and the level of inappropriate behaviour amounting in some cases to corruption would be considerably higher than these figures demonstrate," he said.

Leading administrative law barrister Mark Robinson SC said he had no doubt there was corruption at all levels of government.

"Whenever there is discretionary statutory power exercised that is not openly accountable to external and independent scrutiny, corruption can and will flourish," he said.

Public servants were subject to Senate estimates hearings and independent audits, but proponents of a federal commission said more oversight was required.

APSC says no need for federal watchdog

Despite increasing reports of corruption, there were fewer internal investigations last year with only 0.3 per cent of the workforce formally questioned.

In a statement, the APSC said the majority of employees knew how to report corruption and were aware of the risks.

More than 40 per cent staff who breached conduct rules had their pay cut, while 18 per cent were fired.

The APSC said there were 228 misconduct investigations between 2014-16 that led to terminations. Another 888 public servants were reprimanded.

In the year before the latest APSC survey, 108 public servants were found to be involved in "a form of corruption".

A parliamentary committee stopped short of recommending a federal anti-corruption body in September, instead calling for the Government to give "careful consideration" to the proposal.

Mr Whealy said he was confident the Government would eventually support an independent commission.

"By the time we get to the next election, this is going to be a hot election issue, and I'm hoping there will be bipartisan support," he said.

In a submission to the inquiry, public service commissioner John Lloyd said the majority of misconduct was "of a less serious kind".

The ABC requested an interview with Mr Lloyd.