Over the years, the AMIA bombing has been marked by accusations of cover-ups. All suspects in the "local connection" (among them, many members of the Buenos Aires Provincial Police) were found to be not guilty in September 2004. In August 2005, federal judge Juan José Galeano, who was in charge of the case, was impeached and removed from his post on a charge of "serious irregularities" due to his mishandling of the investigation.[14] In 2005, Catholic Church cardinal Jorge Mario Bergoglio, who became Pope Francis in 2013, was the first public personality to sign a petition for justice in the AMIA bombing case. He was one of the signatories on a document called "85 victims, 85 signatures" as part of the bombing's 11th anniversary.[15]
On 25 October 2006, Argentine prosecutors Alberto Nisman and Marcelo Martínez Burgos formally accused the Iranian government of directing the bombing, and the Lebanese Islamist militant group Hezbollah of carrying it out.[16][5][17] According to the prosecution's claims in 2006, Argentina had been targeted by Iran after Buenos Aires' decision to suspend a nuclear technology transfer contract to Tehran.[18] This has been disputed as the contract was never terminated, and Iran and Argentina were negotiating on the restoration of full cooperation on all bilateral agreements from early 1992 until 1994, when the bombing occurred.[19]
In 2024, an Argentinian court ruled that Iran directed the attack, and that it was carried by Hezbollah. The ruling also characterized Iran as a terrorist state.[20]