The original investigation against former President Fujimori, who has been in Japan since November 2000, was set aside earlier this year for lack of evidence, BBC said Wednesday.
The Human Rights Commission says the sterilizations were carried out between 1995 and 2000 in a bid to reduce poverty in Peru.
Fujimori faces charges of treason, corruption and authorizing death squads, but cannot be tried unless and until he is extradited from Tokyo.