Alberto Nisman was found dead with a gunshot wound to his head shortly before he was due to present evidence in parliament against Cristina Kirchner.
Mr Nisman after a decade long investigation claimed Mrs Kirchner and several government colleagues covered up Iran’s alleged involvement in an attack that left 85 dead.
The 51-year-old days before he died had reportedly told Argentine newspaper Clarin that he “could be dead by the end of this” because of the allegations.
Tens of thousands of Argentines took to the streets yesterday evening to protest Mr Nisman’s death and call for justice.
At least 2,000 demonstrated outside the presidential residence in Buenos Aires and chanted “murderer” and hit against the police barricades.
Mr Nisman’s body was found on Sunday night in his apartment hours before he had been due to testify yesterday at a congressional inquiry.
He had compiled a 300-page dossier about a bombing at the AMIA Jewish community centre in Buenos Aires in 1994 that killed 85 people.
State prosecutor Viviana Fein said preliminary autopsy results suggested “there was no third-person intervention in Nisman’s death.”
However, she added she “could not rule out a provoked suicide” whereby someone forced or blackmailed Mr Nisman to kill himself.
She said: “According to the autopsy, he fired the .22 caliber”.
Senior politicians said they had suspicions about the prosecutor’s death.
Former Argentine Minister of Agriculture Julian Dominguez said: “We want to know which mafiosi sector pushed the prosecutor to take this decision.”
While congresswoman Cornelia Schmidt-Liermann said Mr Nisman had seemed “confident” about the case and had no reason to commit suicide.
She said: “Everybody who had contact with him the last 24 hours says he was confident” about his testimony.
“There is no indication, under any circumstances, that he killed himself.”
The security ministry said a 22-calibre handgun and a single bullet casing were found next to Mr Nisman’s body at his flat in Buenos Aires.
The prosecutor had 10 federal police assigned to his protection because of threats made against him.
Last week Mr Nisman had accused Mrs Kirchner and several of her government colleagues of covering up Iran’s alleged role in the 1994 terror attack.
He claimed the Argentine president along with her foreign minister Hector Timerman had “erased” Iran’s role in return for favourable oil deals.
At the time he said: “The president and her foreign minister took the criminal decision to fabricate Iran’s innocence to sate Argentina’s commercial, political and geopolitical interests.”
Mrs Kirchner published a statement on her Facebook page late on yesterday telling people in Argentina not to believe “lies” about the case.
She said: “There is not just astonishment and question marks, but also a history that is too long, too heavy, too difficult, and above all, very sordid.”
In a statement on her website she also lamented Mr Nisman’s death and said it generated “stupor and questions.”
She initially used the word “suicide” in connection with his death but later put a question mark next to the word.