Foreign Minister Manuel Rodriguez Cuadros told the congressional committee on foreign relations on Tuesday that the case is likely to begin in June or July "at the latest".
Lima has formally requested his extradition on charges of political responsibility for 25 murders by a death squad - for which prosecutors want the former president jailed for 30 years - as well as corruption charges.
Fujimori famously resigned his presidency by fax in 2000 from a Tokyo hotel amid a corruption scandal linked to one of his closest associates, former intelligence chief Vladimiro Montesinos.
The former president then took refuge back in Japan and was granted citizenship as the son of Japanese parents who migrated to Peru.
The Japanese government has stated repeatedly that Tokyo and Lima have no extradition treaty, and that under Japanese law, citizens of the country cannot be extradited.
According to government officials, Peru has asked Japan for Fujimori's extradition twice - in July 2003 and October 2004 - but has not received a satisfactory response from Tokyo.