Doling out the first third of the $700 billion to help stabilize financial firms could cost U.S. taxpayers $64 billion, the Congressional Budget Office said.

The CBO said that the estimated cost of Treasury Department’s implementation of the Troubled Asset Relief Program through Dec. 31 will represent more than a quarter of the funds given out. (Read the report.)

The estimate covers $247 billion in transactions, including $178 billion in capital injections to banks, as well as the special rescues of American International Group Inc., Citigroup Inc. and GMAC.

CBO said the $64 billion figure generally represents the difference between what Treasury paid for the investments or lent to firms and the market value of the transactions. This difference, called the “subsidy rate”, was 26% for the first third of the TARP funds.

The subsidy rate for the government’s special loans in AIG and GMAC are significantly higher than for the majority of TARP transactions. CBO said the estimated cost of the government’s $40 billion loan in AIG would be $21 billion, while the $5 billion GMAC loan would cost $3 billion. –Michael R. Crittenden