As the Federal Deposit Insurance Corp. continues to work a backroom deal with a private equity consortium known as HoldCo, consisting of Dune Capital Management, JC Flowers & Co., and Paulson & Co. , a group that has apparently won the bid for IndyMac Federal Bank , mortgage finance giant Fannie Mae is now holding the deal hostage and threatening to jeopardize the potential sale, according to sources close to the sale negotiations on Tuesday evening.

After IndyMac was seized by regulators this summer, Fannie quickly , and quietly , handed the bank a bill for $1 billion, one source said under condition of anonymity, claiming the failed Pasadena-based thrift had violated representations and warranties on various loans sold to the GSE. The IndyMac-originated loans had early payment defaults or were made under fraudulent conditions, according to the source. IndyMac, now under the control of FDIC officials, responded with an offer in kind to settle the repurchase claims for only $100 million, an offer that the GSE did not accept.

According to sources inside IndyMac and familiar with the transaction, as negotiations on price of the bank’s reverse mortgage unit, Financial Freedom, and concessions on future losses between the FDIC and private buyers heated up these past two weeks, Fannie made it clear that it would not rescind its earlier repurchase claims as part of the deal. The demands mean, ostensibly, that whomever purchases IndyMac’s banking units could be forced to absorb the entire repurchase amount.

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