Justice Minister Daniel Figallo announced the decision, saying Humala had decided to accept a special committee's recommendation against granting Fujimori a pardon on humanitarian grounds.
Fujimori, who governed Peru from 1990 to 2000, was convicted in 2009 of the killings of 25 people by a government-backed death squad in the course of Peru's war against the Maoist Shining Path rebel group.
He has been treated for cancerous lesions on his tongue while in prison, but a medical panel in March said there was no evidence the cancer had returned.