Federal regulators are stepping up their effort against the man who served as President Clinton’s director of the Office of Management and Budget between 1996 and 1998, filing new civil charges against him yesterday seeking more than $91 million that they say he improperly earned after serving in the Clinton administration while running a federally chartered mortgage finance company.

The civil charges filed yesterday by the Office of Federal Housing Enterprise Oversight against the former Clinton budget director, Franklin Raines, and other executives of the Federal National Mortgage Association, say they operated Fannie Mae “in an unsafe and unsound manner,” and showered themselves with “unjustified bonuses.”

The charges, which allege the misapplication of almost two dozen accepted principles of accounting, come two years after the executives were forced out of Fannie Mae amid disclosures of a multibillion dollar accounting scandal that roiled Capitol Hill and the mortgage industry.

The government hopes to recover millions of dollars in bonuses from Mr. Raines and others in the latest attempt to rein in executive compensation, reminiscent of Governor-elect Spitzer’s pursuit of a former head of the New York Stock Exchange, Richard Grasso, whom critics have accused of misleading about his own compensation. Critics call the Fannie Mae scandal worse because it involves potential fraud.

The Office of Federal Housing Enterprise Oversight charges against Mr. Raines and against Fannie Mae’s former controller, Leanne Spencer, and its chief financial officer, Timothy Howard, seek to retrieve at least $115 million in bonuses and civil fines totaling at least $100 million.

“Mr. Raines, Mr. Howard and Ms. Spencer knowingly and … recklessly engaged in misconduct and safety and soundness violations that caused substantial and … material harm and loss,” the oversight office said in a statement. “Such harm was the result of a pattern of misconduct, encompassing both the individual and collective action of these individuals.”

The regulators’ report last spring accuses the executives of manipulating quarterly earning targets in order to reap large multimillion-dollar bonuses they didn’t deserve.

Lawyers for the executives accused federal regulators of being “fatally biased” in filing the charges, painting yesterday’s legal announcement as a politically ulterior attempt to encourage Congress to exercise more authority over the federally chartered mortgage group.

A lawyer for Mr. Raines asked the director of the housing oversight office to recuse himself “immediately and completely from any further regulatory action affecting Mr. Raines,” the Associated Press reported.

Another lawyer, Steven Salky, told the Associated Press the allegations are a “politically motivated attempt to rewrite history,” adding that he is “eager” to refute the government’s charges.

The suggestion that the charges are politically motivated was rejected by Peter Wallison of the American Enterprise Institute, whose recent book is “Privatizing Fannie Mae, Freddie Mac, and the Federal Home Loan Banks.”

“Anyone who knows Jim Lockhart, the head of OFHEO, knows that this is an absurd charge,” Mr. Wallison said. “If that’s all they have with which to defend their clients,” he said, referring to the lawyers’ suggestion of bias, “their clients should be very worried.”

Mr. Wallison said that yesterday’s charges could strengthen class-action suits, as well as provide insight to federal criminal investigators.

The Allan Shivers chair in the law of banking and finance at the University of Texas Law School, Henry Hu, said the alleged misconduct by the mortgage officials, if true, would be “one of the largest frauds in financial history.”

“These executives are paid according to private standards,” Professor Hu said, “but there’s federal backing.”

He added, referring to the federal oversight office’s charges yesterday, “I think it’s perfectly legitimate to try to get the money….There were sure a lot of zeros attached to what Raines got.”

“They submitted six years of misleading and inaccurate accounting statements and inaccurate capital reports that enabled them to grow Fannie Mae in an unsafe and unsound manner,” a statement by the housing oversight office said.