The order on Monday night comes just over a month after he was released from prison, where he was serving 25 years for human rights abuses and corruption, reports the BBC.
The 79-year-old was given a pardon on health grounds but the court in the capital Lima says this does not apply to the new case.
Fujimori has said that he was innocent and would appeal against the court's ruling.
The court also wants to try 22 others for the death-squad killings.
When incumbent President Pedro Pablo Kuczynski granted the pardon in December, there were street protests in Lima.
Fujimori is a deeply divisive figure in Peru, respected by some and reviled by others for his government's crackdown on two violent insurgencies during his tenure from 1990-2000.
An estimated 69,000 people died in the conflict between left-wing insurgents and Fujimori's authoritarian government.
(This story has not been edited by Social News XYZ staff and is auto-generated from a syndicated feed.)
