Outgoing President Ollanta Humala rejected Fujimori's first request for a pardon in 2013. The 77-year-old ex-president is serving a 25-year-sentence for human rights abuses, corruption and sanctioning death squads during his 1990-2000 government.
President-elect Pedro Pablo Kuczynski takes office on July 28. He has said he will not pardon Fujimori, though he left the door open for a law that could let the former president serve his sentence under house arrest because of his age and deteriorating health.
Prime Minister Pedro Cateriano said on his Twitter account that Fujimori had presented a "request for a pardon that will be handled according to the Constitution and the Law."
News of the request came a day after hundreds of people protested in Lima to demand his release. While many Peruvians loathe Fujimori for shutting Peru's congress and committing human rights abuses, others remember him fondly for taming leftist guerrillas and ending hyperinflation.
His daughter, Keiko Fujimori, narrowly lost Peru's presidential runoff last month to Kuczynski, and her party controls congress.