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.
Kirchner, 64, held a press conference in Buenos Aires to hit back at charges from Judge Claudio Bonadio, who ordered her arrest for treason for allegedly covering up Iran's involvement in a deadly 1994 bombing of a Jewish center in Buenos Aires.
Judge Carlos Bonadio ordered on Thursday that Kirchner, who led the country from 2007-2015, be placed in pre-trial detention and stripped of her judicial immunity.
Bonadio's order also targeted other Argentinean officials in the effort to cover up Iran's involvement in the attack, including former Foreign Minister Hector Timmerman, who is Jewish and is now under house arrest due to illness, and former head of the Federal Intelligence Agency Oscar Parrilli, who was charged but not arrested.
Fernandez said in court earlier this year that the deal with Tehran - which was passed by the Argentine Congress but not by Iran's legislature - "had one aim: to allow an investigation into the Iranians accused in the AMIA attack, so that the case could move forward".
Fernandez is accused of trying to cover up Iranian officials' involvement in the 1994 bombing of a Jewish community center, known as AMIA, in Buenos Aires in exchange for favorable trade deals. Nisman accused then-President Kirchner of the cover-up and was found dead hours before he was set to present his case to Congress in 2015.
Congress has 180 days to make a decision.
The death, initially declared as suicide, provoked outcry against government corruption in Argentina. In response, she shut down the Secretariat of Intelligence, replacing it with the Federal Intelligence Agency in March 2015.
Her political clout has since faded with the victory of center-right President Mauricio Macri in elections later that year, but the populist firebrand now seeks a comeback as leading the opposition against Mr. Macri.
The removal of Fernandez's immunity from arrest needs a two-thirds majority vote in the Senate.
"Many of her administration are now on preventive detention and that's why there's many among the members of the previous government that are saying that the judge and the judiciary are persecuting [them] and that they are victims of the administration of [current President] Mauricio Macri".