On Feb. 8, 1967, Boston informed headquarters that Stephen Flemmi was being upgraded to a "top echelon" informant -- even though he was "suspect[ed] of possibly being involved in gangland slayings."
By 1981, the bureau had adopted rules prohibiting such arrangements. "Informants shall not participate in acts of violence" and "shall not initiate a plan to commit criminal acts," the rules said.
Yet in 1983, when Bulger was upgraded to "top echelon" informant, a field memo said he was "the titular head of the Winter Hill mob and as such sits as an equal at the policy-making level" with New England Mafia leaders.
Boston kept headquarters apprised of Stephen Flemmi's rise too, alerting them, in a Nov. 25, 1987, memo that he was also a "policy-making" member of the Winter Hill Gang.
The director's office responded with a message of congratulations for the way the informant was being handled.
Throughout the 1980s, local and state police tried to build a case against Stephen Flemmi and Bulger, but the pair was always one step ahead of them.
The reason: They were being tipped off by Boston agents, testimony in recent criminal cases has revealed.
FBI headquarters also may have lent a hand.
In 1983, for example, FBI agents in Oklahoma suspected the pair in the murder of Roger Wheeler, the head of World Jai Alai, who was shot between the eyes in Tulsa after discovering that someone was skimming money from his business.
When Oklahoma agents sought to interrogate Bulger and Stephen Flemmi, Robert Fitzpatrick, then deputy chief of the bureau's Boston office, deflected suspicion from them and blocked the interrogations.
He was instructed to do so during a meeting in Washington with top FBI officials including Sean McWeeney, head of the FBI's organized crime section under Webster, Fitzpatrick said in a recent interview.
"It was to protect Whitey Bulger," said Fitzpatrick, now retired. "That was part of the discussion."
McWeeney, also retired, did not reply to requests for an interview.
In the end, however, even the FBI could not protect the informers forever.
Today, Stephen Flemmi is serving 10 years for obstruction of justice and other offenses and awaiting trial on federal racketeering charges that link him to 10 murders.
Bulger, still on the run, is also under indictment for racketeering. Federal prosecutors blame him and his gang for 21 killings.
Eleven of them occurred while he was an FBI informant.