In addition, Bank of America said it received subpoenas, interrogatories or civil investigative demands from a number of state attorneys general regarding municipal derivatives transactions from 1992 to the present.
Bank of America said it is cooperating with regulators. It disclosed the various matters in its quarterly report filed with the SEC.
Auction-rate debt has interest rates that reset through periodic auctions. Once thought safe, much of the market has been frozen since February, when Wall Street brokerages stopped supporting the debt.
Earlier on Thursday, Citigroup agreed to buy back more than $7 billion of auction-rate securities and pay a $100 million fine to settle regulatory charges that it fraudulently misled investors about the debt's risk. Other financial companies have also faced regulatory inquiries or charges.
Countrywide, meanwhile, is also under investigation by the FBI, authorities have said. The FBI last month said it had 21 corporate targets in its investigation of potential corporate fraud in the mortgage industry.
California, Connecticut, Florida and Illinois have all sued Countrywide over its lending practices.
Separately, Bank of America said it has bought $525 million of assets this quarter as part of a restructuring of a structured investment vehicle, in a bid to support some money market funds at its Columbia fund unit.
It expects other SIVs to be restructured and this could result in further losses.
Bank of America shares closed down $1.93, or 5.8 percent, at $31.52 on the New York Stock Exchange. They have fallen 24 percent this year.