By Christina Rexrode and Andrew Grossman 

Citigroup Inc. will pay $7 billion to settle the U.S. government's accusations the bank misled investors about the quality of mortgage securities it sold in the run-up to the financial crisis.

The Justice Department on Monday said Citigroup knowingly sold mortgage-backed securities with loans containing "material defects" and concealed that information from investors in what Attorney General Eric Holder described as "egregious" misconduct that helped fuel the 2008 financial crisis.

The settlement, which includes a $4 billion civil penalty, doesn't absolve Citigroup or its employees from facing any possible criminal charges, Mr. Holder said. He declined to say whether the government was pursuing criminal charges.

Citigroup admitted to many of its misdeeds "in great detail" the Justice Department said. A statement of facts released by the government--and agreed to by the bank--detailed a pattern of the bank repeatedly ignoring its own red flags about subpar mortgages and making misrepresentations to investors about the quality of loans being securitized.

On several occasions, bank employees learned that significant percentages of mortgage loans reviewed as part of its "due diligence" were defective. One Citigroup trader, in an internal email cited by the government, stated the bank "should start praying" because so many of the loans were likely to go sour. "It's amazing that some of these loans were closed at all," the email stated.

Despite knowing the underlying mortgages were problematic and might wind up in default, Citigroup pooled the loans into residential-mortgage backed securities and sold them to investors, the government said.

"Citigroup employees often personally ordered the due diligence firms to change the loan grades...from reject to accepted," said Colorado U.S. Attorney John Walsh.

In all, the Justice Department uncovered 45 mortgage-security deals in 2006 and 2007 in which the bank made misrepresentations about the quality of the underlying loans, said Loretta Lynch, the U.S. attorney from Brooklyn.

"Our teams found that the misconduct in Citigroup's deals devastated the nation and the world's economies, touching everyone," Ms. Lynch said, adding the harmed investors included public pension funds, states, cities, religious charities, and hospitals.

"The bank's activities contributed mightily to the financial crisis that devastated our economy in 2008," Mr. Holder said. "Taken together, we believe the size and scope of this resolution goes beyond what could be considered the mere cost of doing business."

In a call with reporters Monday morning, Citigroup Chief Financial Officer John Gerspach declined to comment on whether the bank had asked for release from any potential criminal charges as part of the settlement.

"We believe that this settlement is in the best interests of our shareholders, and allows us to move forward and to focus on the future, not the past," said Citigroup Chief Executive Officer Michael Corbat in a statement.

To resolve the probe, Citigroup will pay a $4 billion civil penalty to the Justice Department, plus $500 million to the Federal Deposit Insurance Corp. and several states. Citigroup also agreed to spend $2.5 billion on "consumer relief," where it will get credit for modifying mortgages for struggling homeowners and similar actions.

The pending settlement and other legal problems have been an overhang for the bank. Citigroup's penalty, unlike a similar settlement between the Justice Department and J.P. Morgan Chase & Co. in November, releases it from potential liability for CDOs, or collateralized debt obligations, not just mortgage securities. The settlement covers residential mortgage-backed securities and CDOs issued in the run-up to the financial crisis, from 2003 to 2008.

The bank has "now resolved substantially all of our legacy RMBS and CDO litigation," Mr. Corbat said in his statement.

Still, the bank faces a continuing probe of whether its Banamex USA unit did enough to stop suspected money laundering in suspicious transactions along the U.S.-Mexico border.

Citigroup also released its second-quarter earnings Monday, with the bank disclosing its profit dropped 96% in the quarter thanks in part to a pretax charge of about $3.8 billion related to the settlement. Still, the company's earnings came in better than analysts' expectations.

Citigroup's $7 billion agreement comes after a long negotiation. The bank in May had opened with an offer to pay $363 million in cash, plus more for "consumer relief," or money the bank will set aside to help customers in financial trouble. The Justice Department came back with a far higher number: $12 billion, including consumer relief.

The bank had argued that it shouldn't have to pay so much because it was a relatively small player in the mortgage-securities market. But the Justice Department lawyers saw Citigroup's conduct as so egregious that it merited a high penalty.

At one point in mid-June, the government came to within a day of filing a lawsuit against the bank.

Citigroup is the second of the U.S. megabanks to settle with the government over mortgage securities. J.P. Morgan settled similar charges in November for $13 billion. Talks between the government and Bank of America Corp. are under way.

The negotiations were seen as a flash point for both Mr. Corbat, who was given the top job in 2012 with a mandate to improve relations with the government, and for Mr. Holder, who has faced constant criticism that his Justice Department has been too soft on banks.

In May, the Justice Department extracted from Swiss bank Credit Suisse Group AG its first guilty plea from a major financial institution in two decades, and French bank BNP Paribas SA pleaded guilty last week to charges over its dealings with countries sanctioned by the U.S.

It has been a tough year for Citigroup so far. In February it disclosed an alleged accounting fraud against its Mexico unit. In March the Federal Reserve rejected its stress-test request for a higher dividend and share buyback, citing a need for the bank to improve its overall risk-management systems.

Write to Christina Rexrode at christina.rexrode@wsj.com and Andrew Grossman at andrew.grossman@wsj.com

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