Obama spelled out his directive in a memo to agency and department directors on Tuesday.
The president said he appreciates the job done by the federal work force and that he understands how the bonuses and other similar salary adjustments are important to employees and their families.
But Obama said that, like households and businesses across the nation, those in the government "need to make tough choices about how to spend our funds."
The freeze takes effect immediately and lasts through the budget ending September 2011.
It does not apply to federal workers who are not political appointees.