The department will draw down money from the budget for the current fiscal year to fill that gap. The agency must now come up with a cost-cutting plan to absorb the loss of those funds this year. Georgia's constitution prevents the agency from running a deficit.
Layoffs and the delay of transportation projects are possible.
A separate state audit concluded that the department's right of way office, which acquires property for road development, doesn't know how much land it owns. The office has sometimes forced Georgians to sell their land and then let it languish, sometimes for years.
Transportation officials said they are halting acquisition of new land through the right of way office for projects that are not slated for construction in the next two to three years.
The audits had been requested by transportation commissioner, Gena Evans, who took over the department last fall. She was hand-picked by Gov. Sonny Perdue to lead the agency, which has been plagued by complaints of mismanagement, delays and promising more projects than its bank accounts could deliver.
Perdue has also requested an outside audit to help sort out the financial mess.
DOT has 5,500 employees and an annual budget of $2.3 billion.
The department was surprised by the size of the hole this year's budget hole. Officials thought the deficit was shrinking. But just a few weeks ago, staff stumbled across contracts and change orders that had never been entered into the state's accounting system. Together they cost the state $360 million.
The audits' findings were revealed at a meeting of the transportation board's finance committee. The full board will meet next week to discuss ways to deal with the shortfall.
"We've got a lot of work to do," Evans told the Atlanta Journal-Constitution. "and this is a long-term fix."