Mortgage finance giants Fannie Mae and Freddie Mac may have lost up to $3 billion from the ma­nipu­la­tion by several big banks of the global interest rate known as Libor, according to an internal government memo.

That was just one more sign Wednesday of the growing rate-fixing scandal, as federal prosecutors and regulators also announced that Swiss banking giant UBS had agreed to pay $1.5 billion in fines for manipulating the rate. U.S. authorities also filed criminal charges against two UBS employees, the first individuals targeted by the widening investigation.

The interest rate — the London Interbank Offered Rate, or Libor — is supposed to reflect the rate at which banks lend to one another and is used as a benchmark for other interest rates around the world. The Commodity Futures Trading Commission was the first to uncover evidence that something was amiss with the rates going as far back as 2005.

The ma­nipu­la­tion likely caused Fannie and Freddie to lose billions of dollars on their holdings of more than $1 trillion in interest-rate swaps, floating-rate bonds, mortgage-backed securities and other assets linked to Libor from September 2008 to 2010, according to a memo from the inspector general for the Federal Housing Finance Agency, the regulator that oversees Fannie and Freddie. The Washington Post obtained the memo Wednesday.

The inspector general recommended that FHFA conduct a thorough review and consider suing the banks involved in the scheme. The memo was reported earlier in the day by the Wall Street Journal.

Although a FHFA spokeswoman said the regulator “has not substantiated any particular Libor-related losses for Fannie Mae and Freddie Mac,” she said the agency is considering the inspector general’s findings and will “continue to evaluate issues associated with Libor.”

UBS is now the second international bank — Barclays being the first — to own up to its role in the rate-fixing. They are among 16 banks, including Bank of America, Citigroup, HSBC and JPMorgan Chase, that submit data to set the daily Libor rate.

Prosecutors say a cadre of traders and senior managers at the Swiss banking giant colluded with at least four other banks and pressured brokers to spread false data to manipulate multiple global interest rates. The changes could have caused banks to appear healthier than they really were during the financial crisis of 2007 and 2008 by suggesting that they were trading with low interest rates. But the actions also could have allowed banks to manipulate financial trades to create profits.

UBS agreed with authorities in the United States, Britain and Switzerland to a combined $1.5 billion settlement — triple the amount that Barclays agreed to pay in June. In addition, its Japanese subsidiary pleaded guilty to criminal charges of felony wire fraud filed by the Justice Department. The agency said it is not prosecuting the parent company because of the bank’s cooperation with the investigation.

However, criminal indictments are being brought against two former UBS traders — one in Britain and one in Switzerland — for conspiracy to manipulate Libor. One of them is also being charged with wire fraud in New York federal court. The traders are the first individuals to face criminal charges in the banking scandal to date, but may not be the last as federal prosecutors ramp up efforts to clamp down on banking misconduct.

“Effective deterrence is only going to be realized when bank officials are indicted, convicted and sent to prison. To that extent, this is a positive step forward. However, it’s a small step,” said James Gurule, a former undersecretary of enforcement for the Treasury Department and now a law professor at the University of Notre Dame.

Gurule took issue with the Justice Department’s decision not to indict the parent company and more of its executives given the broad scope of the problems at UBS.

But Assistant Attorney General Lanny A. Breuer defended the actions at a news conference. “By any fair criteria, this is a very real, a very robust and a very forceful resolution,” he said, adding that the department took into consideration the new leadership at UBS and the bank’s cooperation with the investigation.