NEW YORK (CNNMoney.com) -- The Securities and Exchange Commission filed charges Monday against Bank of America for misleading investors about billions of dollars in bonuses paid to top executives at Merrill Lynch following its purchase of the brokerage giant.

But the SEC simultaneously announced that it would settle with the Charlotte, N.C.-based lender, who will pay a penalty of $33 million as a result.

Calling the settlement a "constructive conclusion" to the controversial subject, Bank of America neither admitted nor denied the charges. The settlement with the SEC will remain subject to court approval.

Regulators alleged that Bank of America failed to disclose plans to as much as $5.8 billion in bonuses for fiscal year 2008 in its proxy statement. Instead, Bank of America told shareholders that Merrill had agreed not to pay year-end performance bonuses, according to the SEC.

"Failing to disclose that a struggling company will pay out billions of dollars in performance bonuses obviously violates that duty and warrants the significant financial penalty imposed by today's settlement," Robert Khuzami, Director of the SEC's division of enforcement, said in a statement.

Merrill's decision to pay big bonuses first came to light in February, after New York State Attorney General Andrew Cuomo accused the firm of "secretly" rewarding executives before its merger with BofA closed.

The subsequent investigation by state officials ultimately led to a string of revelations, including Merrill's decision to move up the date of its year-end bonus payments.

Bank of America chief executive officer Ken Lewis also alleged during the investigation that federal regulators threatened to remove him and other board members if Bank of America backed out of the deal.

Congress waded into the issue shortly thereafter, as lawmakers grilled Lewis, Federal Reserve Chairman Ben Bernanke and former Treasury Secretary Henry Paulson on the matter.

Rep. Darrell Issa, R-Calif., the ranking member for the House Committee on Oversight and Government Reform, said that the SEC's charges against BofA offered a "validation" of the concerns of his fellow committee members.

The committee has been looking into what transpired after BofA agreed to buy Merrill and Issa hinted that the investigation may not be over.

"The circumstances certainly underscore the need for us to continue our investigation of the Bank of America -- Merrill Lynch acquisition and the role officials at the Treasury and Federal Reserve had in pressuring the acquisition to move forward," Issa said in a statement.

Cuomo's office also indicated Monday that Bank of America may not be free from further scrutiny, adding that they were continuing their investigation about whether Merrill's bonuses violated state securities laws.

Separately, Bank of America announced a shake up in some of its top management ranks Monday, including the hiring of former Citigroup (C, Fortune 500) executive Sallie Krawcheck to run the bank's global wealth management unit.

Bank of America (BAC, Fortune 500) shares rose more than 3.5% in Monday afternoon trading.

Talkback: Did Bank of America make a mistake by buying Merrill Lynch?