Prosecutors allege that the now-exiled Fujimori "co-authored" the two massacres and "knew in detail the operations" of the paramilitary death squad known as the Colina group, the attorney general's office statement said.
The Colina group is accused of gunning down 15 people in 1991 during a barbecue at a Lima tenement building. Some of the paramilitary group's members were convicted in the kidnapping and murder of nine students and a professor at La Cantuta University in 1992.
Prosecutors also are accusing Fujimori of the murder of former intelligence agent Mariela Barreto, whose dismembered and decapitated body was found in March 1997, the statement said.
Congress paved the way for the charges Aug. 27 by lifting the constitutional immunity of Fujimori, who has been in his parents' native Japan since November when his 10-year rule collapsed in a growing corruption scandal.
The homicide and forced disappearance charges, which Peruvian officials say constitute crimes against humanity, are the most serious to date against Fujimori, who says he plans to stay in Japan indefinitely.
Fujimori also faces charges of abandonment of office and dereliction of duty, which carry a maximum two-year prison sentence. He denies any wrongdoing and claims he is the subject of "vulgar political persecution" in Peru.
Japan announced Fujimori was entitled to citizenship shortly after he arrived there, and Japanese law prohibits the extradition of its citizens to stand trial for crimes committed in other countries.
Peruvian officials hope the new charges of human rights abuses will help persuade Japan to either extradite Fujimori to Peru, try him in Japanese courts or send him to an international tribunal, such as the one in The Hague, Netherlands.
"There are a series of international treaties to which Japan is a signatory," Prime Minister Roberto Danino told foreign correspondents last week. "When we have the legal route laid out and established, we will push their compliance with the treaties so Fujimori can be brought to justice."
But Japanese officials have reiterated their position that extraditing Fujimori to Peru for crimes allegedly committed in Peru is not permitted under Japanese laws since he is a Japanese citizen.
Under its own laws, Peru cannot make an extradition request until a Supreme Court judge formally accepts the charges against Fujimori and opens investigative proceedings. The court has 15 days to do that.
Japan signed an international treaty against torture in 1999, but it is only obliged to hand over suspects accused of torture that took place after the country joined the pact.
A senior official in Japan's Justice Ministry said Japan has not signed the U.N. treaty on international human rights tribunals and would not bauthorized to extradite Fujimori to an international human rights court.
©MMI The Associated Press. All Rights Reserved. This material may not be published, broadcast, rewritten, or redistributed