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Five years after the housing market crumbled, government officials are still trying to assign blame for the problems that fueled the mortgage boom and bust.

On Wednesday, federal prosecutors in New York took aim at Bank of America. They accused it of carrying out a scheme, started by its Countrywide Financial unit, that defrauded government-backed mortgage agencies by churning out loans at a rapid pace without proper controls. In a civil suit, prosecutors seek to collect at least $1 billion in penalties from the bank as compensation for the behavior that they say forced taxpayers to guarantee billions in bad loans.

Financial firms have been battling chaotic — and at times redundant — litigation related to the mortgage mess. The cases have come from a patchwork of federal agencies, state officials and shareholder suits, some of which have been resolved in multibillion-dollar settlements.

“They never know who’s going to be coming after them next,” said Dan Hurson, a former federal prosecutor who now defends securities cases. “There’s no central traffic cop.”

Still, the public has been frustrated with the limited number of criminal actions that have been filed since the financial crisis. Few cases have taken aim at top executives. Even in the latest case against Bank of America, no company officials were sued as part of the complaint. Angelo R. Mozilo, the former chief executive of Countrywide Financial, never faced criminal charges but did agree in 2010 to pay $67.5 million to settle a civil fraud case brought by the Securities and Exchange Commission.

Mr. Hurson said that the government had yet to overcome the notion that federal authorities were reluctant to pursue the top rungs of Wall Street. The criminal actions to come from the crisis, he noted, have focused on “small-time operators.”

The government, however, has contended that it has aggressively pursued mortgage fraud. As the legal deadline approaches for filing crisis-related cases, President Obama formed a mortgage task force to investigate wrongdoing. The unit recently announced its first case, taking action against JPMorgan Chase over mortgage deals created by Bear Stearns, the firm that JPMorgan bought during the crisis.

The legal problems for Bank of America, however, have taken a deeper financial toll, costing the bank billions in write-downs and settlements. Much of its problems stem from its takeover of Countrywide Financial, once the nation’s largest mortgage lender. The bank also struck a $2.4 billion deal in September to settle a class-action lawsuit over shareholder claims that it misled investors about the 2009 purchase of Merrill Lynch.

In the lawsuit on Wednesday, the Justice Department attacked a home loan program known as the “hustle,” which the bank inherited from Countrywide in 2008 and kept alive through 2009.

Prosecutors say the venture was a symbol of Wall Street’s slipshod standards during the mortgage bubble. According to the lawsuit, Countrywide rubber-stamped mortgage loans to risky borrowers and passed them on to Fannie Mae and Freddie Mac, the two government-controlled mortgage financial giants that guaranteed the loans. The two entities were ultimately stuck with heavy losses and a glut of foreclosed properties.

“The fraudulent conduct alleged in today’s complaint was spectacularly brazen in scope,” Preet Bharara, the United States attorney in Manhattan, said in a statement. “This lawsuit should send another clear message that reckless lending practices will not be tolerated.”

Mr. Bharara filed the civil suit along with the inspector general of the Federal Housing Finance Agency, which oversees Fannie Mae and Freddie Mac. The government watchdog for the bank bailout program, the special inspector general for the Troubled Asset Relief Program, or TARP, also joined the complaint.

In a statement, a Bank of America spokesman said the bank “has stepped up and acted responsibly to resolve legacy mortgage matters; the claim that we have failed to repurchase loans from Fannie Mae is simply false.” The spokesman, Lawrence Grayson, added, “At some point, Bank of America can’t be expected to compensate every entity that claims losses that actually were caused by the economic downturn.”

The case builds on a broader federal crackdown of Wall Street that continues years after the onset of the crisis. In a last-ditch effort to hold financial firms accountable, Mr. Bharara this month sued Wells Fargo over questionable mortgage deals.

The assertions in the Bank of America suit, however, do not shed much new light on the mortgage mess. The Federal Housing Finance Agency last year sued 17 big banks over losses sustained by Fannie Mae and Freddie Mac over different mortgage-related products. The twin mortgage finance companies, also bailed out by taxpayers in 2008 and still controlled by the government, continue to push firms like Bank of America to repurchase billions of dollars in bad loans.

The flurry of litigation, which comes on the cusp of the presidential election, has caused some on Wall Street to question whether the effort is rooted in political motivations.

Other white-collar lawyers say the complaints rehash old claims put forth by private investors. JPMorgan says that the government urged it to buy Bear Stearns, a defense that does not apply to Bank of America, which acquired Countrywide as part of an aggressive expansion effort.

Still, a lawyer close to the Bank of America case, who spoke on the condition of anonymity because the case was continuing, argued that the bank had already repaid Fannie Mae for some of the soured loans in question. Other loans, this person argued, were never before disputed by Fannie Mae.

The lawsuit threatens to impose steep fines on the bank. The Justice Department filed the case under the False Claims Act, which could provide for triple the damages suffered by Fannie and Freddie, a penalty that could reach more than $3 billion.

The act also provides an avenue for a Countrywide whistle-blower, Edward J. O’Donnell, to cash in. Under the act, the government can piggyback on accusations he filed in a lawsuit that was kept under seal until now.

Mr. O’Donnell, who lives in Pennsylvania, was an executive vice president for Countrywide before leaving the company in 2009. The government’s case in part hinges on the credibility of his claims.

In the 46-page lawsuit, prosecutors contend that Countrywide abandoned its lending standards in 2007 with the creation of the “hustle” program. Short for “HSSL,” or “High-Speed Swim Lane,” the program adopted the motto “move forward, never backward,” prosecutors said, citing Countrywide documents.

With the goal of generating a high number of loans, Countrywide tore down internal controls known as tollgates that were in place to slow the mortgage process and root out risky borrowers. The firm at one point removed trained underwriters from the loan process, opting instead to rely on “unqualified and inexperienced” loan processors.

At times, prosecutors claim, loan processors crossed a legal line. Some “repeatedly did manipulate” loan forms, jotting down higher incomes for borrowers so they would qualify for Fannie Mae’s standards.

By early 2008, the lax standards started to show. More than a third of the unit’s loans were defective, a significant jump over the industry standard of about 5 percent.

Despite the poor performance, prosecutors said, the bank sold the loans to Fannie Mae and Freddie Mac and “concealed the defect rates and continued the hustle.”