The regulator for Fannie Mae and Freddie Mac sued UBS AG to recover more than $900 million of losses, alleging that the Swiss bank misled the housing agencies into buying $4.5 billion of risky mortgage debt.

In announcing Wednesday’s lawsuit, the Federal Housing Finance Agency said it plans more lawsuits to recover additional losses by Fannie Mae and Freddie Mac from investments in private-label debt.

Last July, the FHFA issued 64 subpoenas to banks, seeking details about subprime and other mortgage debt that Fannie Mae and Freddie Mac bought when the housing market was healthy.

The UBS case is part of a push by Washington to hold banks responsible for the nation’s housing problems. It is also the latest effort to prop up the government-sponsored enterprises Fannie Mae and Freddie Mac, whose September 2008 federal seizure has so far cost taxpayers more than $135 billion.

“From the issuance of 64 subpoenas last year to the filing of this lawsuit and further actions to come, we continue to seek redress for the losses suffered,” FHFA Acting Director Edward DeMarco said in a statement.

District-based Fannie Mae and McLean-based Freddie Mac remain crucial to the housing market. In 2010, they guaranteed 70 percent of single-family mortgage-backed securities that were issued and provided $1.03 trillion of market liquidity, according to an FHFA report to Congress last month.

UBS spokesman Peter McKillop had no immediate comment. FHFA spokeswoman Corinne Russell declined to comment further.

In May, the government filed a fraud lawsuit accusing Deutsche Bank AG of misleading the Federal Housing Administration into believing that many low-quality mortgages issued by the German bank’s MortgageIT unit qualified for insurance. Deutsche Bank is seeking to have that case dismissed.

According to the complaint against UBS, Fannie Mae and Freddie Mac lost more than 20 percent of their investment in more than $4.5 billion of residential mortgage-backed securities that the bank sold in 16 pools from September 2005 to August 2007.

The complaint, filed in the U.S. District Court in Manhattan, also says UBS failed to do adequate due diligence and hid or misstated the quality of the underlying loans, the quality of the underwriting, and the borrowers’ ability to make payments.

The lawsuit seeks to recoup Fannie Mae’s and Freddie Mac’s losses and undo the purchases, among other remedies.

— Reuters