By Sarah Marsh and Maximiliano Rizzi

BUENOS AIRES (Reuters) - An 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 was found dead in his apartment, authorities said on Monday.

Alberto Nisman, who had been delving into the blast at the AMIA Jewish community center in Buenos Aires that killed 85 people, said Wednesday that Fernandez opened secretive discussions with Iran and at least one of the men suspected of planting the bomb.

He said the scheme was intended to clear the suspects so that Argentina could start swapping grains for much-needed oil from Iran, which denies any connection with the bombing.

Nisman was found dead on Sunday night in his apartment in the posh Buenos Aires neighborhood of Puerto Madero, Argentina's security ministry said. A 22-calibre handgun and a single bullet casing were found next to his body, the 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."

Preliminary autopsy results from the morgue suggested "there was no third-person intervention in Nisman's death," the office of state prosecutor Viviana Fein said in a statement.

Fein told reporters she "could not rule out a provoked suicide" whereby someone forced or blackmailed Nisman to kill himself.

Nisman, who had seemed combative in recent interviews rather than frightened, had been due to take part in what promised to be a tough closed-door hearing in Congress on Monday to explain his accusations. Lawmakers allied with Fernandez said they were ready to grill Nisman about the charges.

On Monday those lawmakers told reporters they were shocked by the news and also suspected more than a straightforward suicide. "We want to know which mafiosi sector pushed the prosecutor to take this decision," said Julian Dominguez, who leads the ruling coalition in the lower house of Congress.

The prosecutor's security guards alerted his mother on Sunday afternoon that he was not answering his front door or phone. She found the door to his apartment locked from the inside and got a locksmith to open it. She found her son's body on the floor of the bathroom and called the police.

'ALONE'

"He was alone in the apartment," prosecutor Fein told reporters. "There are no witnesses."

Officials said the cause of Nisman's death would be announced in the days ahead.

Thousands of Argentines signed up on social media to join marches set to take place throughout the country on Monday night to protest Nisman's death and call for justice.

The Clarin daily newspaper reported that Nisman told the newspaper just a few days earlier, "I could end up dead because of this."

Nisman, who had been receiving death threats for years, said in a separate TV interview he had also been considering increasing his security detail. Israel issued a statement mourning Nisman's death and urging Argentine authorities to carry on his work. Argentina's main Jewish organizations, AMIA and DAIA, praised his "inalterable impulse to get to the truth."

But the judge handling the case of the 1994 bombing criticized 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 courts have accused Iran of sponsoring the 1994 bombing, a charge Tehran denies. In 2007, Argentine authorities secured Interpol arrest warrants for five Iranians and a Lebanese over the bombing.

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

The truth commission pact was struck down by an Argentine court and never ratified by Iran.

Nisman had said the commission was intended to help get the arrest warrants dropped as a step toward normalizing bilateral relations and opening the door to obtaining Iranian oil needed to help close Argentina's $7 billion per year energy deficit.

(Additional reporting by Walter Bianchi and Hugh Bronstein in Buenos Aires and Dan Williams in Jerusalem; Editing by Kieran Murray and Cynthia Osterman)