In a written statement, Pedro Pablo Kuczynski said that he made a decision to release Fujimori, 79, for "humanitarian reasons" as he has "a progressive, degenerative and incurable disease". He remains a divisive figure in Peru.
Kuczynski last week faced a move by the opposition in Peru's Congress to force him from office for graft, but he avoided being deposed due to the votes in absentia of lawmaker Kenji Fujimori - Fujimori's son - and nine other legislators with the Popular Force, which was considered to be the start of an alliance in favour of a pardon.
"The president of the republic... has chose to grant a humanitarian pardon to Mr Alberto Fujimori and seven other people in similar condition", the presidency said in a statement that did not name the other recipients.
He is admired by some Peruvians for combating Maoist rebels, whereas his critics consider him a corrupt dictator.
Kuczynski pardoned Fujimori and seven other persons "in similar condition" on Sunday evening.
Kuczynski is one of several politicians in Latin America to be dogged by allegations of taking illicit money from Odebrecht. He was eventually extradited to Peru and was convicted for leading death squads that massacred civilians.
His two adult children, Keiko and Kenji, lead rival factions of the party, Popular Force, that controls a majority of seats in Congress.
"Instead of reaffirming that in a state of law there is no special treatment for anyone, the idea that his liberation was a vulgar political negotiation in exchange for Pedro Pablo Kuczynski maintaining power will remain forever", he added.
His sister, opposition leader Keiko Fujimori, also expressed her delight.
TV images showed Kenji, who has led calls for his father's freedom, riding in the ambulance carrying Fujimori.
"In coming days, the left may have achieved what Fujimori's supporters have been unable to: a pardon for Fujimori", Chlimper said.
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