On Sunday, hours before he was set to testify before the National Congress about his allegation, he was found dead in his apartment, the country's Ministry of Security said Monday.
Nisman, 51, who had been investigating the Jewish community center bombing that occurred more than 20 years ago, was found in his bathroom with a .22-caliber gun and shell casing nearby, the ministry said.
No cause of death has been released, but according to the Buenos Aires Herald, Security Secretary Sergio Berni and Anibal Fernández, secretary-general to the presidency, said there are signs that Nisman's death was a suicide.
"The forensic investigation is crucial. In forensic science, when you have a body, a cartridge and a weapon, everything leads to one place," Berni said, according to the newspaper. "We have to wait for the judicial to confirm."
Buenos Aires police will conduct tests on Nisman's hands to see if there is gunpowder on them, the state-run Telam news agency reported. Such a test would be necessary to determine whether he committed suicide.
"As the days go by and we have the results from the autopsy, we will be able to determine the cause of death. I can't venture a hypothesis; that wouldn't be prudent," Viviana Fein, the federal prosecutor leading the investigation into Nisman's death, told reporters in Buenos Aires. "I can confirm that there was a gun, a .22-caliber gun. I can confirm that he died due to a gunshot. I cannot confirm further details. I will find those out in the coming days."
Nisman's mother discovered his body shortly before midnight.
The prosecutor had been under the protection of a 10-man security detail, members of which belonged to the Federal Police. The detail called his secretary Sunday afternoon to say he wasn't answering his phone, Telam reported.
When he didn't answer his doorbell and his Sunday newspaper was found on his doorstep, the security detail reached out to his family.
The detail took Nisman's mother to his apartment in Le Parc Tower, a high-rise in the Puerto Madero neighborhood of Buenos Aires, and upon finding the door locked from the inside, with the key still in the lock, Nisman's relatives reached out to a locksmith, the agency reported.
Nisman's mother and a guard later found the prosecutor's body blocking a bathroom door inside his room, Telam said.
Nisman was set to testify to lawmakers behind closed doors on a report alleging that President Cristina Fernández de Kirchner, Foreign Minister Héctor Timerman and other officials had covered up Iran's involvement in the bombing of the Argentine Israelite Mutual Association building. The attack killed 85 people and wounded more than 300.
Fernández de Kirchner and Timerman wanted to cover up Iran's involvement in order to boost trade -- specifically, oil imports and grain exports -- with the Islamic republic, Nisman alleged last week, according to the Herald.
Chief of the Cabinet of Ministers Jorge Capitanich told CNN and other media outlets that Nisman's allegation is "crazy, absurd, illogical, irrational, ridiculous, unconstitutional." Timerman also formally rejected the accusations last week.
Appointed in 2004 by Fernández de Kirchner's late husband, then-President Néstor Kirchner, Nisman told members of the Argentine opposition that he had documents to back his allegations, the Herald reported. He was also expected to divulge sources for his research.
Congresswoman Patricia Bullrich, who represents Buenos Aires in the National Congress' lower house and who organized the hearing, said she spoke with Nisman on Saturday.
"He said he was very threatened and he knew that this was a very heavy topic," she said. "I am very dismayed."
Argentine prosecutors have long accused Iran of involvement in the bombing and requested the arrest of Iranian citizens in connection with it, among them former Defense Minister Ahmad Vahidi, former Iranian President Ali Akbar Hashemi Rafsanjani and Mohsen Rezaie, head of Iran's Revolutionary Guard at the time of the attack.
Iran has denied the charges.
In 2013, Argentine lawmakers approved the creation of a "truth commission" designed to investigate the bombing in conjunction with Iran.
The National Criminal Court is investigating Nisman's death, the Security Ministry said. His body has been sent to a morgue for autopsy, Capitanich told CNN.
Israel's Foreign Ministry, in a statement to media outlets, called Nisman a "brave and prominent jurist who fought ceaselessly for justice" as he worked to expose those behind the 1994 attack.
"The State of Israel voices hope that Argentine authorities will continue with Nisman's activities and make every effort to exact justice on those responsible for the terrorist attacks in Argentina," the statement said.
The Anti-Defamation League called for a full and transparent investigation into Nisman's death, which it labeled "another tragic episode that will extend the decades-long delays in bringing the Iranian masterminds and perpetrators to justice."
"The timing and circumstances of Mr. Nisman's death, coming just days after he released detailed allegations of high-level government attempts to evade his investigation and hours before he was scheduled to present additional details to members of the Argentine Congress, raise serious questions about whether Mr. Nisman's death was related to his work on the AMIA bombing," ADL National Director Abraham Foxman said in a statement.
CNN's Michael Pearson, Iván Pérez Sarmenti, Elwyn Lopez and Robert Lenz contributed to this report.