Prosecutor Sebastián Basso, who replaced the late Alberto Nisman, asked federal judge Daniel Rafecas to issue national and international arrest warrants for Khamenei, according to Argentine paper Clarin.
Basso also requested the application of trial in absentia for the remaining Iranian and Lebanese suspects named in the case.
Some of the high-level officials accused in the bombing case include former Iranian President Akbar Hashemi Rafsanjani, who has since died, then-Foreign Minister Ali Akbar Velayati, and former Intelligence Minister Ali Fallahian.
Others include former IRGC commander Mohsen Rezaee, former Quds Force commander Ahmad Vahidi, former Iranian diplomat Ahmad Reza Asghari, former cultural attaché Mohsen Rabbani, and Imad Mughniyeh, the late Hezbollah operations chief.
The move follows the passage of a law promoted by President Javier Milei last year, allowing trials in absentia in cases involving grave crimes.
The bombing remains Argentina’s deadliest terrorist attack. On July 18, 1994, a truck loaded with explosives detonated outside the Argentine Israeli Mutual Association (AMIA) building in Buenos Aires, killing 85 people and injuring hundreds.