Judge Claudio Bonadio asked lawmakers to remove Fernandez's immunity from prosecution, which she gained when she was sworn in as a senator last week. She was president from 2007 to 2015.
The judge also ordered the arrest of several aides and allies of Fernandez, including former presidency Secretary Carlos Zanni and activist Luis D'Elia on the same charges. Former Foreign Minister Hector Timerman was ordered held under house arrest due to health issues.
Prosecutor Eduardo Taiano said the charge of treason carries a potential prison sentence of 10 to 15 years while aggravated cover-up has a six-year penalty. A vote of two thirds of the Senate would be required to remove Fernandez's immunity from prosecution.
Fernandez and the other defendants have repeatedly denied wrongdoing or involvement in any cover-up involving Argentina's worst terror attack, the 1994 bombing of the Argentine Israelite Mutual Association center in Buenos Aires, which killed 85 people and wounded hundreds. Investigators have linked former Iranian officials to the attack, but Iran has denied any connection with the attack and declined to turn over suspects.
Fernandez was president from 2007 to 2015.