WASHINGTON — The Treasury Department Friday rejected a proposal for Fannie Mae to sell $2.6 billion, or roughly half, of its unused low-income housing tax credits to two unidentified investors believed to be Goldman, Sachs & Co. and Berkshire Hathaway Inc.

The Obama administration told the government-sponsored enterprise that the sale would result in a loss of aggregate tax revenues that would outweigh any savings to the federal government, and that blocking the transaction would better protect taxpayers.

Fannie announced the proposal in its quarterly financial statement, filed Thursday with the Securities and Exchange Commission. The Federal Housing Finance Agency, which regulates the GSE, had approved the transaction, saying, “It is consistent with the conservation of the assets of the corporation.”

Low-income housing tax credits are often used in conjunction with bond-financed housing projects. Fannie Mae said it entered into a “nonbinding letter of intent” sometime before Sept. 30 to transfer the credits.

Although the filing did not name the “unrelated third-party investors” receiving the credits, the two investment companies have been widely reported to be part of the transaction.

Some housing group officials said they were concerned that the credits would be sold at a heavy discount to the investors, further driving down the value of the remaining credits. But Fannie said that under the terms of the proposal, it would transfer to investors the credits at a price that exceeds their current carrying value. It did not provide specific numbers.

If the transfer had been completed, the investors would have been able to take full advantage of the tax credits “for a specific period of time,” Fannie Mae said. It would have received some breathing room on its balance sheet. The credits have rapidly lost their value, adding to the losses that Fannie Mae must report each quarter.

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