The charges stem from an investigation initially conducted by Alberto Nisman, a crusading prosecutor who accused Fernandez of a coverup in 2015 and was later found dead in the bathroom of his apartment.
However, as Kirchner is now a senator, the Argentinian Congress [official website, in Spanish] will have to first vote to strip her of her parliamentary immunity before she can be taken into custody.
Several prominent members of her former government have been detained on corruption charges in recent weeks, including ex-public works minister Julio De Vido and Amado Boudou, Kirchner's vice-president from 2011-2015. Still a key figure in the Argentine left, she blamed her major political antagonist, President Mauricio Macri, a center-rightist, for orchestrating "these maneuvers and ... persecution". But Argentine officials are investigating the possibility that Nisman was killed.
The former president is accused of signing a deal with Tehran to allow Iranian officials suspected of ordering the attack on the Jewish center to be interviewed by Argentine magistrates in Tehran rather than in Buenos Aires.
He has ordered the arrest of Kirchner, her former foreign minister Hector Timerman, and former top aide Carlos Zannini as well as other former officials.
The agreement created a joint commission to investigate the AMIA bombing that critics said was really a means to absolve Iran.
"This is an invented case about acts that don't exist", Fernandez, recently elected a senator, told reporters at the national Congress as allied lawmakers surrounded her.More news: How 'I, Tonya' tackled its controversial domestic violence scenes
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"The case was absolutely paralyzed because Iran does not extradite its compatriots".
Moreover, he said, Iran through the agreement appeared to achieve its goal of avoiding being declared a "terrorist" state by Argentina.
Earlier Thursday, a federal judge had asked Argentina's Senate to remove Fernandez's immunity as a lawmaker so that she could be arrested on suspicion of treason.
The treason allegation unveiled Thursday represented the first time that a judge had requested Fernandez's arrest.
Fernandez now faces a battle over her immunity to prosecution in Congress.
Fernandez and the other defendants have several options to appeal, which could drag the case out for years.