In a letter sent in September that became public on Tuesday, the SEC asked Wells Fargo Controller Richard Levy to explain how Wells Fargo went about valuing its roughly $20 billion portfolio of troubled loans – that it acquired primarily by buying Wachovia.

The SEC's questions, which may represent another headache for Wells Fargo following a sales scandal, relate to assumptions the bank made in determining how to value the loans. On a portfolio of so-called "Pick-a-Pay" mortgages, for example, the discussion focused on metrics such as borrower credit score and loan-to-value.

In recent months, stock analysts at firms including Keefe, Bruyette & Woods and Credit Suisse have raised questions about whether Wells Fargo's earnings are supported by underlying business growth or accounting maneuvers.

"There is this sense they are managing earnings and the way you can manage earnings is if you interpret accounting in beneficial ways at the appropriate moments," said Charles Peabody, analyst at Compass Point Research & Trading. "I don't think that is necessarily a bad thing. The problem is that when you get on that treadmill it's hard to get off it."

Wells Fargo's Levy responded to the SEC's questions in detail in an October letter. His response included tables showing how and why values changed over time. In correspondence the next month, the SEC's senior assistant chief accountant, Stephanie Sullivan, said the agency had completed its review. Valuing such loans "is challenging, and that is the answer that Wells Fargo is offering," said Judy Beckman, an accounting professor at the University of Rhode Island.

The SEC regularly questions companies on their earnings reports. The regulator sent 2,905 such letters to companies during the 12 month period ended June 30, according to a report from Ernst & Young.