Judge Claudio Bonadio also called on the Senate to begin procedures to strip her of her parliamentary immunity, which requires a two-thirds majority.
The 64-year-old former president held a press conference in Buenos Aires to hit back at the charges, saying the order seeking her arrest was "an excess that violates the rule of law."
Kirchner, who has long claimed her legal woes are politically motivated, accused center-right President Mauricio Macri of "manipulating" the justice system to "persecute the opposition."
In a press conference frequently interrupted by applause from her supporters, she described Bonadio's main charge of "treason against the Fatherland" as "an insult to the intelligence of Argentines."
Bonadio also ordered the arrest of former foreign minister Hector Timerman and several other former officials in the Kirchner government, including former top aide Carlos Zannini.
The ex-head of the Federal Intelligence Agency, Oscar Parrilli, was placed under house arrest and ordered not to leave the country.
Cover-up or 'act of foreign policy'?
Kirchner stands accused of signing a 2012 deal with Tehran to allow Iranian officials suspected of ordering the attack on the Argentine Israelite Mutual Association (AMIA) -- which killed 85 people and wounded 300 -- to be investigated in their own country, rather than in Argentina.
Bonadio asserts that this was part of "an orchestrated criminal plan" to cover up the alleged involvement of Iranian officials in return for lucrative trade deals with the Islamic republic.
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The charges have been rejected several times by courts as lacking substance, but the case was reopened in February this year.
The former head of state said in court that a memorandum of understanding with Tehran -- passed by the Argentine congress but not by Iran -- "had one aim: to allow an investigation into the Iranians accused in the AMIA attack, so that the case could move forward."
She has argued in the past that since Iran and Argentina have no extradition agreement, and Argentina does not carry out trials in absentia, there was no other way to proceed with the investigation.
Kirchner told the press conference that the signing of the memorandum in 2012 "was an act of foreign policy that cannot be prosecuted."
"From the legal point of view, it is nonsense -- a real excess that violates the rule of law."
"We have been here for 23 years and no one has been put behind bars for this," she lamented.
"The case was absolutely paralyzed because Iran does not extradite its compatriots. What we did was to act within the framework of international law."
The AMIA attack is the subject of several parallel cases as prosecutors are also looking into whether the country's leadership at the time had conspired to obstruct the investigation.
Among those facing trial separately are former president Carlos Menem (1989-99), the judge who led the investigation for its first 10 years, the ex-head of the intelligence agency, two prosecutors and a representative of the Jewish community.
Kirchner, who stepped down after two terms in 2015, won a Senate seat in elections in October, giving her immunity in a slew of corruption cases stemming from the 12 years she dominated Argentina's politics with her late husband Nestor.
The Senate, which is due to convene on December 10, will now have to consider a vote on lifting her immunity at the judge's request, for which a two-thirds majority is needed.
Kirchner's leftist alliance in the Senate has a total of 32 seats in the 72-seat Senate, but only around a dozen senators are in the Kirchner camp.
Macri's center-right Cambiemos alliance has 25 seats in the upper house.
The case is based on charges first levelled two years ago by crusading prosecutor Alberto Nisman. He was found shot dead in his Buenos Aires apartment on January 18, 2015, four days after formally accusing Kirchner of a cover-up.
The Jewish center bombing case is the most serious for Kirchner, who is facing trial in several other cases involving corruption and money-laundering stemming from her years as president.
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, her vice president from 2011-2015.
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Argentine investigators accuse five former Iranian officials -- including former president Ali Akbar Rafsanjani, former foreign minister Ali Akbar Velayati and ex-Republican Guard head Mohsen Rezai -- of ordering Lebanese Shiite group Hezbollah to carry out that bombing. Iran denies any involvement.
The attack -- which followed a 1992 bombing of the Israeli embassy in Buenos Aires that killed 29 people -- devastated Argentina's Jewish population, the largest in Latin America at about 300,000 people.