Judge Claudio Bonadio accused Kirchner, 64, of seeking to negotiate a deal with Iran to obtain trade concessions in exchange for covering up Tehran's role in a 1994 terror attack on the AMIA Jewish center that killed 85 people.
Ms. Fernandez's vice president and planning minister are already jailed awaiting trial, and another Cabinet official, Legal Secretary and 2015 vice presidential candidate Carlos Zannini, was taken into custody Thursday on Judge Bonadio's orders.
"This accusation is based on an agreement ... that would allegedly allow Argentine judges to interrogate Iranian officials that Argentina claims were involved in that investigation", she said.
Fernandez and members of her government "betrayed traditional and historical national interests and those of the people affected by the attacks" and looked to "gain impunity for Iranian citizens accused in the attack on the AMIA headquarters and to normalize relations between both states", Bonadio wrote in a 491-page complaint.
"We have been here for 23 years and no one has been put behind bars for this", she lamented. "What we did was to act within the framework of worldwide law".
The order is the latest move to resolve a case that's gripped Argentina for years. For that to happen, two-thirds of the legislators must decide to remove Kirchner's immunity for an arrest.
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Kirchner, who was sworn in as a senator on November 29, along with former officials in her government, were accused by prosecutor Gerardo Pollicita of an "aggravated cover-up" of the bombing that is considered a crime against humanity.
Macri's center-right Cambiemos alliance has 25 seats in the upper house.
Nisman was found dead in his home on January 18, 2015.
Cristina Kirchner was the Argentinian president from 2007 to 2015.
She has previously called the case an "absurdity".
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.