By Elizabeth Barber

BOSTON (Reuters) - An ex-FBI agent who testified in the trial of James "Whitey" Bulger was arraigned on Thursday for lying on the witness stand about his efforts to stop the Boston mobster.

Robert Fitzpatrick, a former special agent at the Boston office of the Federal Bureau of Investigation who testified for Bulger's defense in July 2013, pleaded not guilty to six counts of perjury and six counts of obstruction of justice, federal court officials said on Thursday.

A warrant was issued for his arrest and he surrendered to U.S. federal marshals on Thursday morning.

Prosecutors allege Fitzpatrick lied when he testified at trial that the FBI office in Boston rebuffed his insistence in 1981 that Bulger, head of Boston's infamous Winter Hill Gang, was not a real informant for the office and that the FBI should terminate his informant status.

The indictment against Fitzpatrick claims he never advocated that the FBI should withdraw its protections for the Irish-American gangster and start investigating him.

Bulger committed most of his crimes, including 11 murders, in the 1970s and 1980s while acting as an informant for corrupt FBI agents who ignored his activities in exchange for information about the Italian-American mafia, prosecutors have said. Multiple wrongful death lawsuits related to the Bulger killings were filed against the FBI between 1993 and 2003.

Bulger was convicted last year and is serving two life sentences.

Fitzpatrick's handcuffs were taken off as he was shown to his seat in federal court in Boston on Thursday. The 75-year-old former FBI agent, a stout man with a grayish red mustache, was released on a $50,000 unsecured bond and told to surrender his firearms. His next court date is June 10.

Fitzpatrick, who worked for the FBI from 1965 to 1986 and authored the book "Betrayal, Whitey Bulger, and the FBI Agent Who Fought to Bring Him Down," faces up to six years in prison for each count of perjury and up to 10 years in prison for each count of obstruction.

The indictment also alleges that Fitzpatrick over-billed his credentials, including lying that he recovered the rifle used to assassinate civil rights leader Martin Luther King, Jr in Memphis in 1968, as well as personally arrested New England mob boss Gennaro "Jerry" Angiulo in 1983.

During Bulger's trial, Fitzpatrick was aggressively cross-examined by prosecutors, who accused him of fibbing.

(Editing by Richard Valdmanis, G Crosse and Alan Crosby)