Freddie Mac and JPMorgan Chase & Co. are in a dispute over bad mortgages sold by Washington Mutual that may strip JPMorgan of millions of dollars in fees.

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Freddie Mac and JPMorgan Chase & Co. are in a dispute over bad mortgages sold by Washington Mutual that may strip JPMorgan of millions of dollars in fees.

JPMorgan, which took over WaMu’s assets after the Seattle-based thrift collapsed, told Freddie it won’t buy back mortgages sold by WaMu that failed to match promises made about their quality, Freddie said Friday in a regulatory filing.

Freddie, the mortgage-finance company seeking $13.8 billion of capital from U.S. taxpayers, in turn told JPMorgan that it won’t permit the bank to keep the thrift’s mortgage-servicing contracts “unless it assumes the Washington Mutual repurchase obligations,” according to the filing.

Freddie, competitor Fannie Mae, insurers, banks and bond investors have been seeking to enforce contracts that would shift more of the losses from a surge in U.S. foreclosures to the lenders that originally made the loans or to others that provided assurances about their creditworthiness.

Under Freddie’s agreements with banks, the company can seize contracts to service, or manage, outstanding loans for several reasons, including a failure by the servicing bank to repurchase mortgages. Servicers collect mortgage payments and pass them on to other companies and bond investors for a fee that’s typically 0.25 percent a year.

WaMu, the fifth-largest mortgage servicer at the time of its collapse, reported that its contracts to service $441 billion of loans for third parties were worth $6.2 billion on June 30, according to a July statement. Servicing for Freddie, Fannie and government agencies accounted for $252 billion of the loans.

Thomas Kelly, a spokesman for New York-based JPMorgan, which acquired WaMu’s assets and branches in September as the savings and loan became the largest U.S. banking company to fail, declined to comment. JPMorgan is the third-largest servicer, according to newsletter National Mortgage News.

Loan repurchases by sellers to Freddie almost tripled during the first nine months of this year to $1.2 billion and the company may lose more than $1.3 billion because of outstanding “servicing-related obligations” including for buybacks at Lehman Brothers Holdings and IndyMac according to the filing.

Lenders sometimes agree to cover Freddie’s losses instead of repurchasing loans, the filing said.

Freddie, which reported on Friday a record quarterly loss of $25.3 billion, and Fannie own or guarantee more than 40 percent of the almost $11 billion of outstanding U.S. home loans. The government seized the firms in September amid growing losses and promised to inject $100 billion in capital into each, to protect buyers of their debt and mortgage bonds.

Lehman filed for bankruptcy protection in September and IndyMac was taken over by bank regulators in July.