Teresa Tyntalla Contreras, a 62-year-old candy vendor, said she lost a child in one of the massacres for which Mr. Fujimori was convicted. Ms. Contreras said she voted for Mr. Kuczynski when he faced Mr. Fujimori’s daughter Keiko in a runoff in 2016.
“We are angry at Mr. Kuczynski because he has stabbed us in the back,” she said.
Fabián Fernández, 22, a college student who was born halfway through Mr. Fujimori’s administration, called on the government to resign.
“Fujimorismo represents violence, dictatorship, repression, selective killings and bribery,” he said.
Mr. Kuczynski has portrayed his decision as an act of compassion and a gesture toward reconciliation — a move that Mr. Fujimori welcomed in a video recorded from his hospital bed, in which he asked critics for forgiveness — but the president’s critics see a more cynical motive. Mr. Kuczynski survived an impeachment vote last week with help from a faction of lawmakers led by Kenji Fujimori, a congressman and the younger son of Mr. Fujimori, and critics see the pardon as the reward.
The pardon has touched off a wave of resignations, including those of several members of Congress and senior civil servants. On Wednesday, the resignations continued, with the departures of the culture minister, Salvador del Solar; a presidential adviser, Máximo San Román; and the executive in charge of Peru’s public radio and television stations, Hugo Coya.
Daniel Sánchez Velásquez, a Justice Ministry official who resigned earlier in the week, said there was “an essential incompatibility” in Mr. Kuczynski’s wish to provide reparations to victims of violence while “freeing, through a questionable procedure, he who in the context of that terrorist insanity responded with terrible crimes that contributed to the suffering of Peruvian society.”
At a news conference on Wednesday, Mercedes Aráoz, Peru’s prime minister, struck a conciliatory note.
“It is a decision of conscience, and I understand their points of view and we must respect their decisions,” she said of the officials who had resigned.
“We want a peaceful country and one that honestly can cure the wounds from a painful past,” she said. “We are going to work together those who feel cheated by this decision, which was a difficult and painful decision for the president. We are going to insist on having a conversation with the families of the victims. Our doors are open to continue talking about a total reconciliation of our country.”
Mr. Fujimori, who fled to Japan in 2000 as his presidency crumbled under the weight of corruption allegations, tried to mount a political comeback in 2005, traveling to neighboring Chile. Instead he was immediately arrested, and in 2007 he was extradited to Peru. In 2009, he was sentenced to 25 years in prison for his role in two military atrocities committed early in his presidency.
Human rights advocates said this week that they would work to overturn the pardon, both in Peruvian and international courts, though the prospects for such appeals seemed deeply uncertain.
Christian Huaylinos, a coordinator at Aprodeh, a human rights group, cited a precedent in which a court invalidated the pardon of José Enrique Crousillat, a former media baron, after finding that his medical condition was not as severe as he had maintained. (Mr. Crousillat had been recorded taking bribes to run favorable news about Mr. Fujimori.)
But César Nakazaki, a former lawyer for Mr. Fujimori, said the challenge was unlikely to succeed because there was nothing bogus about Mr. Fujimori’s medical conditions.
“All the medical information is consistent and his medical history is in the public domain,” Mr. Nakazaki said.
The international challenge involves the Inter-American Court of Human Rights, of which Peru is a member.
Carlos Rivera, director of the Institute for Legal Defense, said it had asked the court to intervene based on two court precedents. One demanded that Peru not offer amnesty to those convicted in the so-called La Cantuta massacre of 1992, one of two atrocities for which Mr. Fujimori was convicted. The other said that states should not offer pardons or amnesties in cases of serious rights violations.
“We want the court to see that their rulings are not being followed,” Mr. Rivera said.
Diego García Sayán, a former president of the Inter-American Court of Human Rights, said the petition raised novel questions. “This is the first time that someone is presenting a case to the court directly related to pardons,” he said. “There’s more precedent when it comes to amnesties.”
However, Enrique Bernales, a constitutional law scholar at the Pontifical Catholic University of Peru and a former United Nations special rapporteur on the use of mercenaries, was skeptical.
“Given that there is no precedent, that it is a prerogative of the president of the republic and not subject to judicial procedures of any kind, I see it quite difficult and problematic,” he said of the effort to get the international court to reverse the pardon.