BOSTON (AP) — For more than 20 years, FBI headquarters in Washington knew that its Boston agents were using hit men and mob leaders as informants and shielding them from prosecution for serious crimes including murder, The Associated Press has learned.

Until now, the still-unravelling Boston FBI scandal has been portrayed largely as the work of a handful of local agents — mavericks willing to deal with the devil to bring down a Mafia family.

But documents obtained by the AP directly connect FBI headquarters to a pattern of collusion with notorious killers.

The AP found 20 memos from Boston agents to the FBI director’s office, along with six replies, showing that headquarters was told of the abuses and condoned them.

Written between 1964 and 1987, the memos made it clear to Washington that the informants had killed and were likely to kill again, describing one of them as “the most dangerous individual known” in the Boston area. The memos also alerted headquarters that two of the informants were crime bosses, active “at the policy-making level” of criminal enterprises in Boston.

Headquarters also knew that its Boston agents were shielding the informants from other investigative agencies. It knew that one informant who masterminded a murder was allowed to go free as four innocent men were sent to prison in his place.

J Edgar Hoover, William Sessions and William Webster headed the FBI in the years when the memos were written. Hoover is dead; Webster and Sessions declined to be interviewed. It is unknown if any of them read the memos.

It is uncertain who at FBI headquarters did, but someone was paying attention. In the mostly unsigned responses found by the AP, the director’s office welcomed the informants and praised their FBI field handlers.

A spokesman for the FBI in Washington declined to comment, citing ongoing investigations and lawsuits.

The AP found the memos in federal court files and in the records of a congressional committee investigating the abuses.

More than $1 billion in lawsuits have been brought against the government by victims of crimes committed by the informants while they were under FBI protection.

The roots of the scandal lie in the 1960s, when the FBI came under pressure from the public and Congress to crack down on the growing power of the Mafia.

In Boston, FBI agents responded by recruiting two hit men as informants and by forging an alliance with the Winter Hill Gang — vicious thugs eager to seize control of the rackets from the Patriarca Mafia family.

The nature of the arrangement, as disclosed in recent criminal proceedings: In return for information on the Mafia, Boston agents looked the other way as the Winter Hill Gang sold drugs, stole and murdered, even tipping them off when state police or federal drug agents were on their trail.

Both sides got what they wanted. The Patriarca crime family was devastated by federal prosecutions, and the Winter Hill Gang took over Boston-area rackets.

The arrangement stayed secret until 1995, when Massachusetts state police and federal drug agents finally built a racketeering case against the Winter Hill Gang, and the story began to tumble out.

So far, one former FBI agent, John Connolly, has been convicted of racketeering and obstruction of justice and awaits sentencing, and another was granted immunity for testimony. Both had accepted bribes from the informants they were protecting.

The Hit Men

Boston FBI agents recruiting Vincent J Flemmi as an informant knew what he was from the start — and made sure the director’s office did, too.

Flemmi spoke of “plans to become recognised as the No One ‘hit man’ in this area,” Boston agents told Washington in a June 4, 1964, memo.

At least four field memos informed headquarters that Flemmi planned to kill a small-time hoodlum, Edward “Teddy” Deegan, in a dispute over money.

Hours before the murder, Boston agents reported that mob enforcer Joseph “The Animal” Barboza, had joined the plot.

Deegan’s body turned up in an alley in Chelsea, Massachusetts on March 12, 1965. A week later, a memo to headquarters named six men, including Flemmi and Barboza, as the killers and described the murder, right down to who fired the first shot.

But the bureau, it seemed, didn’t want Flemmi in prison. It wanted him on the streets, as an informer.

On June 4, 1965, FBI records show, the director’s office demanded a progress report. Was he ready to inform?

Yes, Boston replied, adding that Flemmi was suspected in eight murders and that “from all indications, he is going to continue to commit murder”.

Soon, FBI memos show, agents also recruited Barboza, convincing him that his Mafia employers had turned on him.

In a June 20, 1967 memo, Boston agents told headquarters that Barboza was the most dangerous man in Boston — “a professional assassin responsible for numerous homicides”. He was also unreliable, Boston reported — a man willing to encourage perjury to avoid a long prison term. He had also vowed never to incriminate his friend, Flemmi.

But with the promise of a light sentence for the Deegan murder, Barboza became star witness in three Mafia trials. A Massachusetts jury trusted his word and convicted six men in the Deegan case. Flemmi and two others identified as the killers in the memos to FBI headquarters were never charged.

Instead, FBI files show, the bureau stood by as Barboza’s false testimony convicted four men who were innocent of the murder. Two died in prison. The others were released in recent years, exonerated when the scandal finally broke.

Barboza had implicated two of them to settle street grudges. The other two were known mob figures.

After the convictions, a July 31, 1968 field memo requested commendations for Barboza’s handlers. Hoover sent a personal reply:

“The successful prosecution of these subjects was a direct result of your noteworthy development of pertinent witnesses.”

In return for his testimony, Barboza was released after five months and relocated with a new identity.

Before long, however, he was threatening to recant his testimony unless given $9,000 for plastic surgery to change his appearance.

If Barboza recanted, convictions “might be overturned and plunge the government into protracted and acrimonious litigation”, federal prosecutors Edward F Harrington and Walter T Barnes warned their supervisor in Washington. In their February 12, 1970 memo, they urged that Barboza be given the money.

Six months later, Barboza did recant — but soon changed his mind and stood by his original story.

Barnes, now retired, said that, as best he can recall, some money was approved for Barboza. At the time, he had no reason to believe Barboza’s testimony was false, he said. Harrington, now a federal judge in Massachusetts, declined comment.

In 1976, the New England Mafia found Barboza and exacted its revenge, shotgunning him on a San Francisco street.

Flemmi died in prison in 1979 after Massachusetts authorities convicted him of attempted murder in another case.

The Bosses

James J “Whitey” Bulger and Vincent Flemmi’s big brother, Stephen, nicknamed “The Rifleman”, were just rising in the crime world when Boston agents recruited them as informants. Agents told headquarters what kind of men they were.

On February 8, 1967 for example, Boston agents told the director’s office that Stephen Flemmi was being upgraded to a “top echelon” informant — even though he was “suspected of possibly being involved in gangland slayings”.

By 1981, the bureau had adopted new rules saying that informants “shall not participate in acts of violence” or “initiate a plan to commit criminal acts”.

Yet in 1983, when Bulger was upgraded to “top echelon”, 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.

Throughout the 1980s, state police tried to build a case against Stephen Flemmi and Bulger, but the pair was always one step ahead of them. The reason: Boston agents tipped them off, testimony in recent criminal cases has revealed.

There is evidence that FBI headquarters sometimes lent a hand.

In 1983, FBI agents in Oklahoma suspected the pair in the murder of Roger Wheeler, the head of World Jai Alai, who was shot in Tulsa after discovering that someone was skimming money from his business.

When Oklahoma agents sought to question Bulger and Stephen Flemmi, Robert Fitzpatrick, then deputy chief of the bureau’s Boston office, blocked the interrogations.

He was instructed to do so during a meeting in Washington with top FBI officials, Fitzpatrick told the AP.

“It was to protect Whitey Bulger,” said Fitzpatrick, now retired.

However, even the FBI could not protect the informers forever.

Today, Stephen Flemmi is serving 10 years for obstructing justice and other offences. He awaits trial on federal racketeering charges linking him to 10 murders.

Tipped by an FBI agent, Bulger fled and remains at large. He is under indictment for racketeering and blamed, with his gang, for 21 killings — 11 while he was an informant.