The U.S. Treasury Department expects to lose $29 billion on the bailouts stemming from the financial crisis, with most of the losses in its housing finance program and the “cash for clunkers” initiative, The New York Times reported.

In a report released yesterday, the administration said it expected a $17 billion loss from its investments in General Motors, Chrysler and the auto finance companies, as well as a $46 billion loss from housing programs like the mortgage modification program known as the Home Affordable Modification Program. Those losses are tempered by an estimated profit of approximately $22 billion the Treasury expects from common stock it will receive from the proposed AIG restructuring.

Treasury officials have declared the bailout a success, emphasizing that much of the program’s money has been returned and that losses are now likely to be less than once expected. The cost, the report says, is far below the $350 billion that the Congressional Budget Office once estimated. “Because of the success of the program, TARP will likely cost a fraction of this amount,” the report said.

Recently, the Congressional Budget Office put the cost at $66 billion. And, after the bailout, the government will still be left with its investments in Fannie Mae and Freddie Mac, the government-backed housing finance companies. The report said Fannie and Freddie were expected to cause “substantial losses,” but it noted that they were financed using other funds, not the troubled asset funds.

 The bright spots, according to the report, were the bank paybacks. Nearly 80 percent of the money given to banks has been paid back. The Treasury also received $26.8 billion from banks through interest payments on the investments as well as from the sale of warrants the government received in the banks.