Kevin Ryan, 51, was one of nine U.S. attorneys whose firings were investigated by Justice Department Inspector General Glenn Fine.
U.S. attorneys are the chief federal prosecutors and litigators in each of 93 federal court districts around the country.
The inspector general's report concludes that the removal process under former Attorney General Alberto Gonzales was "fundamentally flawed" and that partisan political considerations may have been a factor in the firing of several of the U.S. attorneys.
The report calls for appointment of a special prosecutor to look into whether any criminal offenses were committed and whether any high officials lied during testimony on the firings. Attorney General Michael Mukasey appointed a special prosecutor today.
But the document says that in the case of Ryan and one other U.S. attorney, the firings appear to have been justified because of performance concerns.
The report says that internal Justice Department evaluations indicated there were serious morale problems and attrition of longtime prosecutors under Ryan's tenure.
Fine wrote, "We found nothing inappropriate about the department's decision to remove Ryan....The evidence was clear that Ryan was removed because of concerns about his management of his office."
Ryan now heads San Francisco Mayor Gavin Newsom's Office of Criminal Justice. He was not immediately available for comment.
Ryan was replaced by an interim U.S. attorney, Scott Schools, and then by Joseph Russoniello, who took office in January. Russoniello had previously served as U.S. attorney under President Reagan from 1982 to 1990.
The U.S. attorney's office for Northern California has branches in San Francisco, Oakland and San Jose and handles criminal cases and civil cases involving the government in coastal California from Monterey to the Oregon border.
The report states that Ryan was the only one of the nine U.S. attorneys who declined to be interviewed in connection with the inspector general's probe.
But it says that during the 2006 internal Justice Department evaluation, Ryan told Gonzales' chief of staff, Kyle Sampson, who supervised the firings, that the process was unfair and that the department was not considering the office's "great work on some cutting-edge cases...in a very difficult environment and with strained resources."