By Sarah Marsh and Maximiliano Rizzi

BUENOS AIRES (Reuters) - 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.

Alberto Nisman, who had been delving into the blast at the AMIA Jewish community center in Buenos Aires that killed 85 people, said last Wednesday Fernandez had opened a secret back channel to a group of Iranians suspected of planting the bomb.

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

"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 Argentine Security Ministry said in a statement.

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.

AUTOPSY PLANNED

"In the coming days we will determine the cause of death with an autopsy," prosecutor Viviana 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 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 Cabinet Chief Jorge Capitanich had said Nisman's allegations were "crazy, absurd, illogical, irrational, ridiculous, unconstitutional".

Israel's Foreign Ministry issued a statement on Monday mourning Nisman's death and urging Argentine authorities to carry on his work.

Argentine courts have accused Iran of sponsoring the 1994 bombing, a charge the Islamic Republic 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 jointly investigate. She said at the time that the pact 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 against the Iranian suspects 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.

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