As Fernández is a senator, Congress would first have to vote to strip her of parliamentary immunity for an arrest to occur. The judge, Claudio Bonadio, also indicted and ordered house arrest for Fernández’s Foreign Minister Héctor Timerman, the 491-page ruling said.
Fernández called a news conference in Congress to deny wrongdoing and accuse Bonadio and President Mauricio Macri of degrading the judiciary.
“It is an invented case about facts that did not exist,” she said, dressed in white.
Timerman’s lawyer could not immediately be reached for comment.
While removing immunity from lawmakers is rare in Argentina, Congress voted on October 25 to do so for Fernández’s former planning minister Julio de Vido and he was arrested the same day. De Vido is accused of fraud and corruption, which he denies.
Argentina’s legislature has entered a period of judicial recess until March but can be convened for urgent matters.
Fernández and her allies have been the focus of several high-profile cases with arrests and indictments since centre-right Macri defeated her chosen successor and was elected president in late 2015.
Fernández left office just a few months before the Congress in neighbouring Brazil impeached another leftist female leader, Dilma Rousseff, for breaking budget laws.
The cover-up allegations against Fernández gained international attention in January 2015, when the prosecutor who initially made them, Alberto Nisman, was found shot dead in the bathroom of his Buenos Aires apartment.
An Argentine appeals court a year ago ordered the re-opening of the investigation.
Nisman’s death was classified as a suicide, though an official investigating the case has said the shooting appeared to be a homicide. Nisman’s body was discovered hours before he was to brief Congress on the bombing of the AMIA centre.
Nisman said Fernández worked behind the scenes to clear Iran and normalize relations to clinch a grains-for-oil deal with Tehran that was signed in 2013. The agreement created a joint commission to investigate the AMIA bombing that critics said was really a means to absolve Iran.
Argentine, Israeli, and US officials have long blamed the AMIA attack on Hezbollah guerrillas backed by Iran. Tehran has denied links to the attack.
Earlier on Thursday, two lower level allies of Fernández were arrested based on the same ruling from judge Bonadio: Carlos Zannini, a legal adviser, and Luis D‘Elia, the leader of a group of protesters supporting her government.
Zannini’s lawyer, Alejandro Baldin, told local media the detention was “arbitrary, illegal and ran over constitutional and individual rights,” after leaving a police station in Rio Gallegos, where Zannini was held.
D‘Elia’s lawyer, Adrián Albor, told radio station AM del Plata that Bonadio had no respect for the law, rights, justice. “They are coming for everyone in the previous government.”
Bonadio wrote in his ruling that evidence showed Iran, with the help of Argentine citizens, had appeared to achieve its goal of avoiding being declared a “terrorist” state by Argentina.
The crime of treason is punishable by 10 to 25 years in prison, Argentina’s maximum sentence. The next step in the case would be an oral trial and sentences can be appealed on first instance, which could be a long process.
Macri’s leader in the Senate, Federico Pinedo, said on Twitter that Congress would analyze the request to strip immunity “with sincerity and responsibility.”
Macri’s coalition performed better than expected in October 22’s mid-term elections, gaining seats in Congress, but it is not clear if lawmakers will vote to strip Fernández’s immunity. Fernández, who governed from 2007 to 2015, finished second to a Macri ally in the Buenos Aires province Senate race but won a seat under Argentina’s list system. She was sworn in last week.
She was also indicted in late 2016 on charges she ran a corruption scheme with her public works secretary. Fernández has admitted there may have been corruption in her government but personally denies wrongdoing.