A federal judge today ordered the government to pay more than $101 million in the case of four men who spent decades in prison for a 1965...

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BOSTON — A federal judge today ordered the government to pay more than $101 million in the case of four men who spent decades in prison for a 1965 murder they didn’t commit after the FBI withheld evidence of their innocence.

The FBI encouraged perjury, helped frame the four men and withheld for more than three decades information that could have cleared them, U.S. District Judge Nancy Gertner said.

She called the government’s argument that the FBI had no duty to get involved in a state case “absurd.”

Peter Limone, Joseph Salvati and the families of the two other men who died in prison had sued the federal government for malicious prosecution.

They argued that Boston FBI agents knew mob hitman Joseph “The Animal” Barboza lied when he named the men as killers in the 1965 death of Edward Deegan. They said Barboza was protecting a fellow FBI informant, Vincent “Jimmy” Flemmi, who was involved.

The four men convicted on Barboza’s lies were treated as “acceptable collateral damage” because the FBI’s priority at the time was taking down the Mafia, their attorneys said.

A Justice Department lawyer had argued that federal authorities couldn’t be held responsible for the results of a state prosecution and had no duty to share information with the officials who prosecuted Limone, Salvati, Henry Tameleo and Louis Greco.

“It took 30 years to uncover this injustice, and the government’s position is, in a word, absurd,” the judge said Thursday.

“No lost liberty is dispensable,” Gertner told the packed courtroom. “We have fought wars over this principle. We are still fighting these wars.”

Salvati and Limone were exonerated in 2001 after FBI memos dating back to the Deegan case surfaced, showing the men had been framed by Barboza. The memos were made public during a Justice Department task force probe of the FBI’s relationship with gangsters and FBI informants James “Whitey” Bulger and Stephen “The Rifleman” Flemmi.

Limone and Salvati stared straight ahead as the judge announced her ruling. A gasp could be heard from the area where their friends and family were sitting when Gertner said how much the government would be forced to pay.

The men’s attorneys had not asked for a specific amount in damages, but in court documents they cited other wrongful conviction cases in which $1 million was awarded for every year of imprisonment. Gertner ordered the government to pay $101.7 million.

Justice Department lawyer Bridget Bailey Lipscomb declined immediate comment on the ruling.