Nisman had been investigating the death of 85 people in the bombing of a Jewish centre in the capital, Buenos Aires, in 1994 – a probe which involved several prominent government figures, including Ms Kirchner.
He had brought allegations against Ms Kirchner, claiming she helped cover up the alleged involvement of Iranian agents in the 1994 bombing of the Jewish centre in return for a trade deal with Tehran.
In 2006 Nisman, acting as Argentina’s special prosecutor, formally accused Iran of directing the Lebanese militia Hezbollah of carrying out the bombing. Both Iran and Hezbollah denied any involvement.
Ms Fernandez said on Thursday she was “convinced” that Nisman’s death was not a suicide.
‘Not a suicide’
In a letter published by the state news agency Telam, Fernandez said questions about Nisman’s death “have been converted into certainty. The suicide [I’m convinced] was not a suicide.”
The letter contrasts with one she wrote Monday in which she had said his death was a suicide.
Nisman, 51, was found slumped in the bathroom of his apartment with a bullet wound in his head.
He was lying next to a 22-calibre handgun and a bullet casing.
His death came days after Nisman gave a judge a 289-page report alleging Ms Fernandez secretly reached a deal to prevent prosecution of former Iranian officials accused of involvement in the 1994 car bombing of the Jewish centre, an attack that killed 85 people.
He was expected to testify to congress about his investigation hours before his death.
The government has dismissed Nisman’s allegations as “weak” and “baseless.”