Fannie Mae said Wells Fargo will pay USD 541 million in the fourth quarter to resolve repurchase requests on certain loans originated prior to 2009, and was credited for prior repurchases.
Wells Fargo, the fourth-largest US bank by assets, said it had accrued the cost of the agreement on September 30.
The settlement resolves Fannie Mae's claim that Wells Fargo overstated the quality of mortgage securities it sold the quasi-public mortgage finance giant in the run-up to the 2008 financial crash.
"This agreement represents a fitting conclusion to our year of hard work to put legacy issues in the rear view mirror and begin 2014 focused on improving the future of housing finance."
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Shares in Wells Fargo dipped 0.1 per cent to USD 45.46 in early trade.
In addition to the Wells Fargo settlement, Fannie Mae has reached resolutions this year with a number of lenders on repurchase issues and other matters, including Bank of America (USD 11.6 billion), CitiMortgage (USD 968 million) and JPMorgan Chase (USD 670 million).
Both companies remain under US government "conservatorship," with the US Treasury maintaining control through its preferred stock in both companies.