Fujimori's family had pleaded for the pardon on humanitarian grounds, saying the former three-term president had undergone five surgeries for cancer of the tongue, the Los Angeles Times reported Friday.
President Ollanta Humala said he refused to grant the pardon because Fujimori was not suffering from "an incurable or degenerative disease" and because he exhibited a lack of remorse.
The 74-year-old Fujimori was elected president in 1990, but fled to Japan in 2000 during an investigation of his intelligence chief. In 2005, he moved to Chile, where he was arrested and deported to Peru.
He was convicted in 2009 of ordering massacres in which 25 dissidents were killed in 1991 and 1992. He also was convicted of ordering the kidnapping of an investigative journalist.