Alberto Nisman said Iran was attempting to set up intelligence-gathering stations in Brazil, Chile, Colombia, and other countries in the region.
Mr Nisman is investigating a bomb attack that killed 85 people in a Jewish centre in Buenos Aires in 1994.
Iran has always denied involvement in the attack.
But in an indictment handed to a federal judge in Buenos Aires on Wednesday, Mr Nisman repeated the often-made claim that Iran sponsored the bombing.
And he accused Iran of a nefarious project in the wider region.
"I legally accuse Iran of infiltrating several South American countries to install intelligence stations - in other words espionage bases - destined to commit, encourage and sponsor terror attacks like the one that took place against Amia," Mr Nisman was quoted as saying, referring to the Jewish centre bombed nearly 20 years ago.
He said the countries targeted included Brazil, Paraguay, Uruguay, Chile, Colombia, Guyana, Trinidad and Tobago, and Surinam.
And he claimed that Mohsen Rabbani - the Iranian former cultural attache in Buenos Aires who Argentina blames for the Amia attack - was co-ordinating the alleged infiltration operation.
In February Argentine legislators approved an agreement with Iran to set up an international truth commission to investigate the Amia attack.
The Argentine government proposed this commission as a way to reactivate investigations into the bombing, but the opposition and some Jewish groups in Argentina have criticised it.
Argentina has issued arrest warrants for several Iranian nationals and a Lebanese national in connection with the bombing.
An Argentine prosecutor has accused Iran of trying to infiltrate countries in Latin America to sponsor and carry out "terrorist activities".