Prosecutors claim Peron, the third wife of the former president Juan Domingo Peron, signed three decrees that cleared the way for acts of state terrorism during her rule between 1974-1976. She was ousted by a coup in March 1976.
Maria Estela Martinez de Peron, known as Isabel, has lived in exile in Spain since 1981 and assumed office after the death of her husband.
However she struggled to hold onto power as political violence spread between left-wing guerillas and death squads in Argentina.
Rights groups say many members of the "Triple A" squad were later recruited by the military to help carry out its systematic crackdown on dissent after it came to power.
Adolfo Perez Esquivel, who won the 1980 Nobel Peace laureate for his human rights work, told The Associated Press he believed the Triple A, was effectively part of a state structure and thus the beginnings of state-backed terror.
|"Once and for all, we have to get to the bottom of this problem and find out how this terrorism was generated by the state"|
Adolfo Perez Esquivel, former Nobel prize winner
"Once and for all, we have to get to the bottom of this problem and find out how this terrorism was generated by the state," he said. "The search for the truth must go in every direction."
According to government figures, more than 11,000 people were killed during military rule, but human rights groups put the death toll at 30,000.
Change of scope
Two suspected members of the "Triple A" squad, including a former top aide to Peron, have been arrested over the last week in connection with other cases.
There was no immediate reaction from Peron but her lawyer, Atilio Neira, told Argentinian radio that he was awaiting the final resolution of the judge's arrest order.
Felipe Noguera, a political analyst said that dozens of former police and military officers have been summoned for questioning since Argentina's Supreme Court in 2005 annulled a pair of 1980s amnesty laws that hindered the prosecution of human rights cases.
"What might be different is that her surname is Peron," he said. "So this seems to drive home the point that a lot of violence against the left wing started during the Peronist time before and not during the junta."
Previous efforts to bring alleged human rights abusers to justice focused on crime committed during the dictatorship and not before.