Employees at the Aboriginal and Torres Strait Islander Commission (ATSIC) and its Services (ATSIS) unit are afraid they will lose their jobs once the group is absorbed into the mainstream.

ATSIC and ATSIS wind up in less than a fortnight.

South East Queensland commissioner Rob Williams says there is a lot of uncertainty about the delivery of services after the handover.

Mr Williams says many staff members feel left in the lurch.

"They're uncertain about where they'll be going and as many of them are saying, if they're treating us like this now... how will they treat us when we go to the mainstream departments?" he said.

"Will it be a worry that they'll just get our money and then in 12 months time they'll reclassify the jobs?"