Fujimori also insisted that his policies were necessary at a time when the government was battling the Maoist Shining Path rebel group.
The former Peruvian leader has been accused in relation to three incidents that took place during the "dirty war" against the Shining Path.
On November 3, 1991, a group of armed and masked soldiers burst into a party in the Lima suburb of Barrios Altos, killing 15 people, including an eight-year-old boy.
Several months later, nine university students and their professor were rounded up by the same "La Colina" squad, taken to a deserted area of the city and executed with shots to the back of the head.
Fujimori is also charged in relation to the the kidnapping of a Peruvian journalist working for a Spanish newspaper and a businessman, both critics of his government.
Speaking on Wednesday, Fujimori said: "I've been sitting here for more than a year, the only president ever tried by the judiciary of his country.
"I've been indicted because of the policy that I followed, a policy that Peruvians know was one of pacification."
"It's the first time a head of state is tried because of his policy, a policy that even today and after a fierce campaign of lies, insults and disinformation against me, has been acknowledged as one that facilitated a victory against terror."
If convicted, Fujimori faces 30 years in prison.
He is already serving a six-year prison sentence for abuse of power in an unrelated case.
Fujimori fled to Tokyo in 2000 while still president amid a deepening corruption scandal and sent his resignation letter by fax from his hotel.
Japan considered Fujimori, whose parents were Japanese, to be a national and refused to extradite him.
He stayed there for the next five years before flying to Chile in 2005 where he was arrested. Two years later he was extradited to Peru.