The accusation advances the case against Kirchner that was being pursued by late prosecutor Alberto Nisman before he died mysteriously on the eve of congressional hearings on his allegations.
Nisman, 51, was found in his Buenos Aires apartment with a gunshot to the head after alleging that Kirchner ha d protected high-ranking Iranian officials from prosecution over the bombing in exchange for oil.
A new team of three prosecutors plus a coordinator was named to take over the politically charged case on Friday.
The prosecutors promptly endorsed Nisman's conclusions, accusing Kirchner and Foreign Minister Hector Timerman of mounting a cover-up and violating their duties.
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The accusation now goes to the judge in the case, Daniel Rafecas, to decide whether to call Kirchner to make a statement.
The bombing at the Argentine Jewish Mutual Association, or AMIA, killed 85 people and wounded 300, the deadliest such attack in Argentina's history.
After the initial investigation ended with no convictions, Nisman was named in 2006 to reopen the case.
On January 14, four days before he was found dead, Nisman filed a 300-page report accusing Kirchner and Timerman of colluding to shield the Iranian suspects.
His death was initially labeled a suicide, but suspicion has fallen on Kirchner's government.
The president has suggested Nisman was manipulated by disgruntled former intelligence agents who then killed him to smear her.