In September, a team of forensic experts issued a report concluding that Mr. Nisman had been murdered. The report contradicted the findings of another team of experts, convened during Mrs. Kirchner’s tenure, which concluded that Mr. Nisman had most likely killed himself.
Mrs. Kirchner has long denied any wrongdoing, including any involvement in Mr. Nisman’s death or collusion with Iran. (Mr. Nisman’s death is the subject of another investigation.)
Judge Bonadio urged the Senate to lift Mrs. Kirchner’s immunity from arrest as an elected senator, so that she could be jailed to face the charges: aggravated concealment and obstruction of justice as well as treason.
He argued that if she remained free, she could “hinder judicial actions as well as the discovery of the truth.”
Argentine senators enjoy immunity from detention, but the protection does not shield them from prosecution.
A Senate committee has 60 days to consider whether to lift her immunity, and then the full Senate would have up to 180 days to vote. The request must be approved by two-thirds of the senators present.
Approval could be an uphill battle because Mr. Macri’s governing party — where Mrs. Kirchner’s critics are concentrated — lacks a majority.
The Senate leader, Federico Pinedo, who is from Mr. Macri’s party, wrote on Twitterthat when the request to strip Mrs. Kirchner of her immunity enters the Senate, “we will analyze it with seriousness and responsibility.” He added, “This is not about carrying out party politics but rather to make sure that institutions function properly.”
But Mrs. Kirchner’s allies accused the government of Mr. Macri, long her political nemesis, of working with judges to destroy her legacy.
“It is clear that we are in a scenario of political persecution of the leadership of the opposition,” Agustín Rossi, who was defense minister under Mrs. Kirchner and is now a lawmaker, told a local radio station.
Mrs. Kirchner was president in 2013, when Argentina and Iran signed a memorandum of understanding that called for a commission to jointly investigate the bombing. The agreement never came into effect, and it was declared unconstitutional in 2015.
On Thursday, Judge Bonadio said there was enough evidence to charge Mrs. Kirchner and her former allies with treason, because they had sought “impunity for the Iranian nationals accused of the attack on the AMIA headquarters and to normalize relations between the two states,” referring to the community center, the Asociación Mutual Israelita Argentina.
The judge also approved similar charges against several associates of Mrs. Kirchner: Héctor Timerman, the former foreign minister; Carlos Zannini, who was essentially Mrs. Kirchner’s chief of staff; and a community activist, Luis D’Elía, among others.
Some Argentine Jews, who overwhelmingly believe that Mr. Nisman was murdered, expressed support for Judge Bonadio’s decision.
“Thee detentions show that Nisman’s complaint had solid elements,” said Ariel Cohen Sabban, the head of the Delegación de Asociaciones Israelitas Argentinas, a group that is close to AMIA and was critical in getting the case reopened. “It is a revindication of Nisman’s work.”
Mrs. Kirchner will not be the first member of her administration to face efforts to remove her immunity. Julio De Vido, a former planning minister, was stripped of the immunity he enjoys as a member of the Chamber of Deputies, the lower house of Parliament, and turned himself in to authorities on graft charges in October.
Iran has long denied any involvement in the AMIA bombing. Mr. Nisman, before his death, had filed a criminal complaint accusing Mrs. Kirchner and members of her government of trying to shield Iranian officials which includes an embargo of 50 million pesos ($2.9 million) on the former president’s assets, of playing a role in the attack as part of a deal that would supply Iranian oil to Argentina. Judge Bonadio’s indictment on Thursday is based on that complaint.