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(Adds details on judges declining to hear case)
BUENOS AIRES Feb 3 (Reuters) - An Argentine prosecutor found dead in mysterious circumstances last month had drafted a request that President Cristina Fernandez be arrested for conspiring to derail his probe into the deadly bombing of a Jewish center, the investigator into his death said on Tuesday.
The papers were found in the trash at Alberto Nisman's apartment while his property was being scoured for clues over whether the father-of-two committed suicide or was murdered.
He was found in a pool of blood with a single bullet to the head on Jan. 18.
"The drafts are in the file," Viviana Fein, the lead investigator into Nisman's death, told a local radio station.
The request for Fernandez's arrest, which the prominent pro-opposition daily newspaper Clarin said Nisman drafted in June, was not included in his final 350-page submission to the judiciary delivered days before his death. Instead Nisman called for Fernandez to face questions in court.
On Monday, Fein's office had denied the existence of the document containing the arrest request and the government denounced a Clarin story about it as "garbage".
Cabinet Chief Jorge Capitanich even dramatically tore up a copy of the paper in his daily news briefing. But on Tuesday, Fein backtracked, saying there had been a misunderstanding between her and her office, and the documents did exist.
"They are properly incorporated into the case file, nothing is missing," Fein said of the papers on Tuesday.
Nisman spent almost a decade building up a case that Iran was behind the 1994 attack on the Argentine Israelite Mutual Association (AMIA) that killed 85 people. Iran's government has repeatedly denied the allegation.
Nisman had been due the day after his death to answer questions in Congress about his allegations that Fernandez sought to cover up Iran's involvement in return for Iranian oil. Fernandez has called the claim "absurd".
Argentine judges are proving reluctant to take on a case some are calling a "judicial hot potato". Two judges turned down hearing the case on Monday, including one who is already presiding over separate charges of attempts to derail the investigation into the 1994 bombing.
The other cover-up charges involve ex-President Carlos Menem, who ruled the South American country from 1989 to 1999.
Fernandez, who had come under fierce criticism for her handling of Nisman's death, is currently on a trip to China. (Reporting by Richard Lough and Sarah Marsh; Editing by Will Dunham, Kieran Murray, Toni Reinhold)
