Some of the nation’s largest banks are getting sued by federal regulators over mortgage bonds. Read the full story after the jump!

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(WSJ)–The federal regulator for mortgage giants Fannie Mae and Freddie Mac is preparing to sue some of the nation’s largest banks over soured mortgage bonds in a bid to recoup billions of dollars in losses from the failed investments, according to people familiar with the matter.

The Federal Housing Finance Agency, which is charged with conserving the assets of the failed mortgage giants, could file the lawsuits in the coming days, these people said. The suits are likely to allege that mortgages that were securitized by Wall Street firms and other issuers misled investors about the quality of the loans.

The FHFA filed the first of what could be around one dozen lawsuits in July against UBS AG, seeking $900 million in damages. UBS, in a statement at the time, promised to “vigorously” defend against all charges in court. The lawsuit alleged that UBS made false statements about 16 mortgage-backed securities that it sold to Fannie and Freddie from fall 2005 to summer 2007, including overstatements of borrowers’ capacity to repay loans.

The agency’s acting director, Edward J. DeMarco, declined to discuss the lawsuits in an interview last week but said there were “more to come.” An FHFA spokeswoman declined to comment on Thursday.

The FHFA issued 64 subpoenas last year to issuers and servicers of mortgage-backed securities in what has become one of the largest investigations to date of potential securities fraud from the mortgage boom and bust. The FHFA didn’t disclose its targets at the time.

The inquiry has focused on the “private label” securities based on subprime and other risky loans that were originated by mortgage companies, packaged by Wall Street firms, and then sold to investors. Many of the mortgage securities were made up of subprime loans and mortgages requiring little or no documentation of a borrower’s income, which deteriorated dramatically during the housing meltdown.

Fannie and Freddie couldn’t purchase those loans directly, but they were allowed to invest in slices of those securities that carried triple-A ratings. Fannie and Freddie were among the largest investors in those securities. At the end of July, they held nearly $78 billion and $149 billion, respectively, in securities that weren’t backed by a government-related entity. Private-label securities have been among the poorest performing mortgages.

The suits come as the potential statute of limitations for the FHFA to take such actions draws near next week, according to people familiar with the matter. The FHFA placed Fannie and Freddie into conservatorship, a legal process similar to bankruptcy restructuring, three years ago on next Wednesday.

The subpoenas issued last year could have been used to access loan files and other documents that would show how the loans underlying the securities didn’t match the materials used to market the investments. That subpoena power gives the FHFA a big advantage over private investors, which have had a harder time gaining access to the loan files that are critical to filing such lawsuits.

The U.S. government has spent $141 billion to keep Fannie and Freddie afloat. The initial losses that triggered the conservatorship were driven heavily by the sharp drop in the value of risky mortgage securities, but over the past two years defaults on loans purchased by Fannie and Freddie have driven more losses.

The companies began increasing their purchases of private-label securities early last decade in order to boost profits while satisfying government mandates to support affordable housing. In 2005, Freddie Mac purchased $180 billion in private-label securities, up from $24 billion four years earlier.

The growth of the Wall Street securitization machine steadily ate into the firms’ market share for buying and selling loans as securities. That gradually prompted the companies to loosen their own loan standards to become more competitive.

Fannie and Freddie have already recouped around $18 billion from banks since the start of 2010, according to company filings with the Securities and Exchange Commission. Those are for loans that the companies purchased from banks and packaged into their own securities that were then sold to investors.

Other private investors have sought to recoup losses from banks. In June, Bank of America reached an $8.5 billion settlement to resolve certain claims brought by investors. The bank didn’t admit wrongdoing in the settlement. On Tuesday, the FHFA filed a motion that would allow it to intervene in the case.

The FHFA also regulates the nation’s 12 home-loan banks, which serve as major sources of funding for hundreds of banks. At least five of those institutions have filed lawsuits seeking to recoup billions in losses from Wall Street firms.

News of the filing deadline for the lawsuits was first reported Thursday night on the website of the New York Times.