Unions have met with Aboriginal and Torres Strait Islander Services (ATSIS) management to discuss the fate of 1,200 employees after the Federal Government's announcement on Thursday that the agency will close.

ATSIS was established last year to provide services to the Aboriginal and Torres Strait Islander Commission and administer programs according to policies set by ATSIC.

The deputy national president of the Community and Public Sector Union, Jenness Gardner, says employees are still waiting to hear about their fate.

Ms Gardner says ATSIS management is also waiting to hear from the Federal Government about the future of the employees.

"The difficulty from staff's perspective is ATSIS itself doesn't have a time about when the Government will be announcing what will be happening to those 1,200 people, so we have 1,200 people across Australia at the moment who don't actually know where they'll be working, what their terms and conditions will be and, in some instances, whether or not they will have a job," she said.