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 (FNM) 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, Calif.-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.

A spokeswoman for Fannie Mae declined to comment on the bad loan claim, or their role in the sale negotiations. David Barr, spokesman at the FDIC, also declined comment on the details surrounding the IndyMac sale.

As of this week, it is believed that HoldCo is using this billion-dollar outstanding repurchase claim to push down the sale price with FDIC officials. And even after the deal is announced -- expected to come perhaps as early as Wedensday afternoon -- Fannie and HoldCo could still be duking it out behind the scenes on what is actually owed for the bad loans.

Fannie Mae had signaled in August of 2008 that it would be aggressively pursuing repurchase claims on Alt-A loans. In a press statement at the time, the GSE said it would be “ramping up defaulted loan reviews to pursue recoveries from lenders, focusing especially on our Alt-A book.” Following through on that sort of threat is often tough to do, however, according to one industry source, because you could end up hurting a vital originator.

“Pushing strong repurchase claims on any lender of decent size can help put them under,” said the source, a secondary market mortgage executive that asked not to be identified. “But it looks like Fannie decided it could try to push those claims onto the FDIC’s books.”

Additionally, sources in the analyst and investment banking community have privately suggested that Treasury has been equally vocal with them about their unwillingness to hand over a heavily-regulated financial entity such as IndyMac to a group of private financial firms with little experience in managing the intricate world of banking rules.

Treasury had privately pushed the FDIC to find a single bank as the buyer for IndyMac as a whole, yet a last-ditch effort by the banks regulators failed, sources suggested. According to sources working for IndyMac on the current potential sale, after the original December 13th bidding deadline had passed, US Bancorp (USB) was encouraged with a heavy hand by government officials to buy the bank and its various parts, but declined.

Sources familiar the FDIC negotiation say Dune chairman and co-CEO Steven Mnuchin’s tenured relationship with his former Goldman boss Hank Paulson is one of the driving factors behind the FDIC’s apparent decision to allow consideration of a private equity firm on this deal. The FDIC hopes with Dune in the lead, it will help influence Paulson and the Treasury to sign off on the deal.

That is, of course, if Fannie Mae doesn’t get in the way first.

-- Paul Jackson contributed to this story.

Teri Buhl is an investigative journalist covering Wall Street who writes for the New York Post Sunday Business. Previously she was on the edit team of Doubledown Media writing about Hedge Funds and Bank Trading for Trader Monthly Magazine.