Sam Levin in San Francisco

Wednesday 4 January 2017 16.45 ESTLast modified on Wednesday 4 January 2017 16.47 EST

A senior US attorney who was involved in the prosecution of Native American activist Leonard Peltier has requested that Barack Obama grant clemency, with a rare plea that has energized the campaign to free the high-profile indigenous prisoner.

James Reynolds, who supervised a key part of the case against Peltier, who claims he was wrongfully convicted of the 1975 murders of two FBI agents, wrote to the president that clemency for the 72-year-old would be “in the best interest of justice in considering the totality of all matters involved”. 

“There seems to be no point in taxpayers paying his room and board,” Reynolds, 77, said by phone on Wednesday. “It’s time to call it quits.” 

The letter is an extraordinary development for the Native American activist who has been incarcerated for more than 40 years. Civil rights activists and indigenous leaders have long argued that he faced a deeply flawed and unfair trial. 

The clemency push from a former US prosecutor, which is highly unusual, comes as Obama has continued to pardon or commute the sentences of hundreds of prisoners in his final weeks in office, raising hopes that he will also release political activists jailed for decades.

Peltier’s conviction stems from the American Indian Movement’s siege of the site of the Wounded Knee massacre where the US army slaughtered hundreds of Lakota people in 1890. The actions at the Pine Ridge reservation in South Dakota, which began in 1973 and protested broken treaties, prompted an aggressive response from the FBI. 

Peltier, who is serving two life sentences, arrived in June of 1975, and soon after two FBI agents entered private property and sparked a shootout. The special agents, Jack Coler and Ronald Williams, were killed during the confrontation, along with Joseph Stuntz, a Native American.

According to Peltier’s attorneys, who filed a clemency request last year, federal agents made false statements and affidavits, coerced witness statements and deliberately withheld crucial ballistics reports. A prosecutor eventually admitted in court that the US attorney’s office “can’t prove who shot [the agents]” and claimed that Peltier was guilty of “aiding and abetting” in the shooting. 

Reynolds was appointed US attorney in 1976 and oversaw the case’s appeal when much of the evidence that raised serious doubts about the government’s case were revealed. 

The former prosecutor’s letter to Obama does not address the underlying conviction, and in an interview, he declined to say whether he believed Peltier is innocent. 

But Reynolds said it was wrong for Peltier to remain behind bars after 40 years, particularly considering that prosecutors ultimately considered him an accomplice in the crime. “You’re not really participating in the crime yourself. Just because you’re there, you’re going to get nailed.” 

Citing Peltier’s motives, Reynolds added, “he didn’t go out there with the intention to kill anybody. He was trying to protect his people.” 

Cynthia K Dunne, a former assistant US attorney who is representing Peltier, said she has never heard of a case of a federal prosecutor requesting clemency.

“It’s really incredibly extraordinary to have the lead prosecutor on the case stand up,” she said, noting that the FBI has continued to oppose Peltier’s release. “It takes a lot of strength to take on the institution.”

Dunne, who communicates regularly with Peltier, said he was pleased to learn of Reynolds’ letter, but didn’t want to get his hopes up given past disappointments: “It’s just a horrible time to be waiting and not knowing.” 

The renewed fight for clemency comes at a time when the Standing Rock tribe’s fight against an oil pipeline in North Dakota has become an international flashpoint for indigenous rights. Local law enforcement’s harsh tactics and aggressive prosecutions have drawn parallels to the government’s treatment of Peltier. 

The Obama administration’s recent decision to deny a key permit for the Dakota Access pipeline has further sparked hope that he may seek to release Peltier and cement his legacy on indigenous rights. 

Time is running out before the inauguration of President-elect Donald Trump, who is not expected to continue Obama’s records of clemency grants and pardons. 

Peltier’s request for clemency is not a pardon appeal, but simply asks that Obama reduce the sentence. “If he doesn’t take action before 19 January,” Dunne added, “Mr Peltier will die in jail. He’s too frail and too sick to make it much longer in the prison system.”