The Argentine prosecutor who accused President Cristina Fernandez of orchestrating a cover-up in the investigation of Iran over the 1994 bombing of a Jewish community center has been found dead in his apartment, authorities said on Monday.

Special prosecutor Alberto Nisman was due to participate in a closed-door session with Congress Monday over his claim last week that de Kirchner and Foreign Minister Hector Timerman covered up a deal with Iran.

He said they promised to absolve Iranian officials accused of masterminding the 1994 bombing on a Buenos Aires Jewish center that left 85 dead, in return for deliveries of much-needed oil from Iran.

Nisman, who was Jewish, was found shortly before midnight (0300 GMT) in a pool of blood in his bathroom, prosecutor Viviana Fein confirmed Monday. A 22-calibre handgun and a single bullet casing were found next to his body, the Argentine Security Ministry said.

"Everything indicates it was a suicide," National Security Secretary Sergio Berni told local television. "We have to see if gunpowder is found on his hands."

"Alberto Nisman was found dead on Sunday night in his flat on the 13th floor of the tower Le Parc, in the Buenos Aires district of Puerto Madero," the ministry said in a statement.

Federal prosecutor Viviana Fein told Telam, Argentina's official news agency that they were able "to confirm that it was a gunshot wound, .22 caliber," but added that it was too early in the investigation to know what had happened.

The ministry said Nisman's security guards had alerted his mother on Sunday afternoon that he was not answering his front door or phone, and the Sunday papers were still on his doorstep.

Nisman's mother found the door to his flat locked from the inside and had to get a locksmith to open it. She found her son's body on the floor of the bathroom, blocking the entrance, and called the police.

"Next to Nisman's body ... a 22 calibre handgun was found, together with a bullet casing," the ministry statement said.

Nisman, who local media said was 51, had been due to take part in a closed-door hearing in parliament on Monday to explain his accusations against Fernandez.

The Clarin daily reported that just a few days earlier, he had told the newspaper, "I could end up dead because of this." Nisman, in a separate TV interview, had also been considering agreeing to have his security detail increased

"In the coming days we will determine the cause of death with an autopsy," Fein told journalists gathered at the scene in the early hours. "I ask for seriousness, I ask for prudence."

Lawmaker Patricia Bullrich told television channel TN that members of parliament would meet on Monday morning to discuss the situation.

The judge handling the case of the 1994 bombing criticised Nisman late last week for taking it upon himself to "initiate an investigation without judicial control" and said the evidence he put forth was flawed.

Argentine Cabinet Chief Jorge Capitanich had said Nisman's allegations were "crazy, absurd, illogical, irrational, ridiculous, unconstitutional."

Argentine courts have accused Iran of sponsoring the 1994 bombing, a charge Iran denies.

In 2013, Fernandez tried to form a "truth commission" with Iran to jointly investigate the bombing. She said at the time that the pact would reactivate the probe, but Israel and Jewish groups said it threatened to derail criminal prosecution of the case.

The truth commission pact was later struck down by an Argentine court.

Nisman had said the truth commission was intended to help get Interpol arrest warrants dropped against five Iranian suspects as a step toward normalizing bilateral relations. In 2007, Nisman told Haaretz that the Iranians had tried to bribe many countries, mostly from Africa, to vote against the Interpol decision.

Israel's Foreign Ministry offered its condolences over Nisman's "death under tragic circumstances." In a statement on Sunday, the ministry's spokesman Emmanuel Nahshon described Nisman as a "brave, venerable jurist, who fought undaunted for justice, and acted with great decisiveness to reveal the identities of the perpetrators of the terrorist attack and those who sent them."

"The State of Israel expresses hope that the Argentine authorities will continue Nisman's activities and will make every possible effort to put those responsible for the attack in Argentina to justice," he added.

It is currently unclear how Nisman's death will affect the outcome of the investigation commanded by Federal judge Rodolfo Canicoba Corral. The magistrate evaluated the removal of Nisman during the last few days, as result of what he considered a lack of serious evidence on the alleged cover-up operation by President Cristina Fernández de Kirchner and other pro-government figures.

In addition, Canicoba Corral said that some of the evidence gathered by Nisman was gathered without his direct order, and that the attorney committed excesses in his duty, especially regarding the telephone hearings of suspects. Nisman’s accusations were rejected by government officials, who considered it a political maneuver.

Meanwhile, relatives of the 85 victims of the AMIA bombing attack will have to face another judicial struggle following 20 years without justice.