Public servants have told the Community and Public Sector Union they feel they've been forced to play a reactive role to issues emerging within Aboriginal and Torres Strait Islander communities due to a major shortfall of staff and a continuously growing workload.

A survey of more than 100 staff at the National Indigenous Australians Agency has shown more than three-quarters felt they were dealing with excessive workloads.

There was also frustration over staff being unable to visit the communities they are assisting due to COVID-19 travel and health restrictions, adding further stress to the role.

But the federal agency has denied the union's claims, adding the survey size isn't indicative of the wider sentiment.

It said it offered staff a range of support services, including free counselling and coaching services.

National deputy secretary Beth Vincent-Pietsch said the issues had been reported prior to the pandemic but had only become more concerning since.

"The community and our members want to make sure the agency is in a position to work with First Nation Australians [and] to do that the NIAA needs more staff and resourcing," she said.

"The truth is government gravely underestimated the needs of the agency upon inception and have taken no steps over the last two years to rectify this mistake.

"By failing to do this the Morrison government is hurting its staff, communities, and the important work that staff in the agency undertake. This government must invest in the NIAA to ensure that Aboriginal and Torres Strait Islanders get the most out the agency aimed at serving them."

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In last year's public service census, nearly a third of staff at the agency who responded indicated their workload was "well beyond" their capacity - a figure 9 per cent higher than the average public service response.

While there had been significant improvements to its wellbeing score compared to the previous year, the results indicated staff had felt there were serious communication issues within the agency.

An agency spokesperson denied there was a staffing shortage and said levels had remained consistent over the agency's two-year existence.

The spokesperson conceded the health crisis had changed the way it worked.

"COVID-19 has presented a number of challenges to the way we operate and demands have been placed on staff to adapt and respond," a spokesperson said.

"The NIAA is supporting staff by encouraging flexibility and providing support for staff to adapt to new ways of working, including virtual community engagement where necessary."

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