FRANKFURT-- Deutsche Bank AG has agreed to pay $55 million to the U.S. Securities and Exchange Commission to settle allegations it hid paper losses of more than $1.5 billion during the financial crisis that began in 2008.

The giant German lender said it didn't admit or deny the allegations and that no charges were brought against individuals in the matter.

"The SEC acknowledged the bank's cooperation throughout the investigation," Deutsche Bank said in a statement Tuesday.

The SEC said in a separate statement Deutsche Bank has underestimated certain risks by between $1.5 billion and $3.3 billion.

Like its main rivals, Deutsche Bank has been entangled in several regulatory investigations into past misbehavior. The lender in April paid a record $2.5 billion fine to U.S. and U.K. authorities for having tried to manipulate interbank interest rates, known as Libor.

Investors at the bank's shareholder meeting last week lashed out at senior management, and co-Chief Executive Anshu Jain in particular, for the many lawsuits and slow progress resolving them.

The allegations behind the settlement announced Tuesday date to late 2008 and early 2009. A whistleblower at the time alleged the bank didn't update the market value of certain credit default swap transactions, known as super senior trades. The whistleblower alleged the bank thereby masked mounting losses as the market value sank.

Deutsche Bank said Tuesday that it didn't update the transactions' market value because it believed at the time that there was no reliable method for measuring them amid illiquid market conditions during the crisis. The bank said it had since enhanced policies, procedures and internal controls regarding the valuation of illiquid assets.

Stefan Krause, an executive at Deutsche Bank who was finance chief at the time of the alleged mispricing, said in late 2013 that "the bank valuations and financial reporting were proper during the period in question and the allegations of fraud are wholly unfounded."

The Wall Street Journal reported last year that an examination by the Federal Reserve Bank of New York found that the bank's giant U.S. operations suffer from a litany of serious regulatory-reporting problems that the lender had known about for years but not fixed, citing Fed documents it has reviewed.

Deutsche Bank is trying to move beyond its period of scandals and alleged malfeasance. It unveiled a new strategy in late April designed to boost its profitability and share price.

In another positive move for the bank, a Frankfurt prosecutor last week cleared Deutsche Bank executives of possible involvement in an alleged carbon-trading scheme. German media reports recently suggested that some senior executives at the bank knew that individual traders were allegedly involved in a tax-fraud scheme in the market for carbon credits.

Deutsche Bank said last week it was informed by the public prosecutor's office in Frankfurt "that based on the documents regarding the CO2 matter provided by Deutsche Bank on April 24, 2015, there is no reason for the Public Prosecutor to open an investigation against members of Deutsche Bank's management board."

Jean Eaglesham contributed to this article.

Write to Eyk Henning at eyk.henning@wsj.com

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