An Argentinian prosecutor was murdered four days after he formally accused the then president Cristina Fernández of covering up the role of Iranian officials in connection with the country’s deadliest terror attack, a border police investigation has found.

The report, obtained by the Associated Press, bases its conclusions on controversial new evidence and sharply contradicts earlier official findings that Alberto Nisman likely killed himself.

Nisman, 51, was found dead on 18 January 2015, with a bullet in his right temple. A .22 caliber pistol was found next to him.

The crusading prosecutor had led the investigation into the 1994 bombing of a Jewish community centre, which killed 85 people.

Coming just days after Nisman challenged Fernández, his death became a politically charged controversy. Allies of Fernández suggested Nisman took his own life because he couldn’t back up his allegations. Many other Argentinians insisted he had been murdered. It triggered anti-government protests ahead of the 2015 presidential election.

Fernández has insistently denied any wrongdoing and says her government had no role in Nisman’s death. The initial police reports and autopsies concluded there was no sign anyone else had been present when he died. While the national forensics team said there was no concrete evidence it was a homicide, the federal police said the lawyer shot himself in his bathroom.

Federal prosecutor Eduardo Taiano told the AP that Nisman’s death was the most complicated criminal case he had ever investigated. Taiano, who took over the stalled case from another judge in 2016 following a supreme court order, requested a multidisciplinary border police team take a fresh look after an investigation that had been highly questioned for mishandling of evidence and other irregularities.

Taiano said that the agency, whose main role was to guard borders and fight drug trafficking, was chosen because it hadn’t been involved in the earlier, much-questioned investigation.

The border police report says Nisman was beaten by two people who drugged him and placed him in front of his bathtub. While one of the attackers held him under the armpits “as in a hug” the other placed the gun on his head and shot him. It was about 2:46am on a Sunday.

The investigation listed key evidence that wasn’t mentioned in previous reports: Nisman’s nasal septum was broken, he had suffered blows to his hip and other areas, and ketamine, a drug with strong anaesthetic properties, was in his body.

The new report concludes that the attackers tried to stage a suicide, but it notes that other experts throughout the series of investigations never found any traces of gunpowder on Nisman’s hands.

The 1994 bombing of the AMIA Jewish community centre in Buenos Aires killed 85 people and injured hundreds. Fernández’s government struck a 2013 accord with Iran, which was portrayed as a way to reach the truth behind the attack, but the deal, which was approved by congress, was later ruled unconstitutional by an Argentinian court. Nisman believed Fernández was using the deal with Iran to secretly negotiate and help shield the Iranian officials allegedly behind the attack.

Taiano told the AP that he would compare the new report with previous ones and decide whether to treat Nisman’s death as a murder, suicide or induced suicide.

A report by forensic experts on behalf of Nisman’s family in 2015 also argued that the prosecutor did not shoot himself. However, their report said only one attacker carried out the killing by holding Nisman’s right hand and pulling the trigger to make it look like a suicide.

The fatal shot was fired from a gun that had been loaned to Nisman by aide Diego Lagomarsino, a computer technician who said the prosecutor asked for the weapon because he feared for his and his daughters’ lives.

A forensic report sent by Lagomarsino’s defence to Taiano contends Nisman shot himself standing in front of a mirror and then fell back, hitting his head. It says there is no proof Nisman was under the effects of ketamine and argues he suffered injuries on his left hip and ankle several hours before his death. A lesion on his bottom lip could have happened while the body was being transported, it says. The death was said to have taken place between 8am and noon, several hours later than estimated by the border police report.

Taiano said a major challenge for the investigation was contamination of the crime scene. More than 60 people walked carelessly in Nisman’s luxury apartment for several hours after the body was found by his mother and security guards.

In addition, Nisman’s mobile phone and computer were tampered with to delete any traces of the information and calls that he received in the hours before his death. And the apartment building’s security cameras had not been working for days before he died.

“The challenge is very complex,” Taiano said. “If this had been investigated differently from the start, this would be a whole different thing.”

Federal police officers who were in charge of Nisman’s security are also being investigated, and experts say the differing conclusions on what happened could point to negligence or the mishandling of information.