The SEC has admitted to accounting issues in the past and for 2010 turned to the Department of Transportation to handle its bookkeeping, The Washington Post reported Friday.
But problems persisted with the GAO citing "a litany of issues" in a report released this week.
"Frankly, the SEC should have prevented or detected [the problems] on its own," GAO Managing Director Jeannette Franzel said.
SEC Chairwoman Mary Schapiro recently told a Senate panel that "years of underinvestment in financial system technology" had helped create the situation. The bookkeeping at the SEC was "unacceptable" she said.
Some worry the SEC could be spending beyond its means, but the GAO said its audit had caught the mistakes, which mounted into the hundreds of millions of dollars. The agency's books are now correct, the GAO said.
The mistakes for 2010 included the failure to break out a $452 million item on its financial statement.
The SEC also has hundreds of millions of dollars in fines and penalties on its books it expects it will never collect.
Of $657 million owed to the agency in fines and restitution charges, the agency expected to collect only $82 million, the newspaper said.