The federal government is caught up in a second data privacy scare, this time involving a massive data-set on more than 96,000 of its public servants amid fears their confidential information might not be secure.

In the second potentially serious Commonwealth data breach to become public in less than a week, the public service's workplace authority has confirmed that it has withdrawn the data gathered in its massive annual employee census from public view.

96,000 public servants may have been affected in the most recent data privacy scare.

It is feared that identification codes for departments and agencies could be used to identify the individual public servants who filled in the census, the largest workplace survey undertaken in Australia, on condition of anonymity.

The data has been taken down from official websites to be washed of any features that could be used to breach the privacy of government officials.