Analysts surveyed by Thomson Financial had expected a loss of just 68 cents a share.
Fannie Mae president and chief executive officer Daniel Mudd says "credit performance has continued to deteriorate" and more losses are expected.
Fannie Mae has slashed its dividend from 35 cents a share to 5 cents a share and plans to hike fees, cut operating costs by 10 percent by the end of next year and take other money-saving steps.