The National Criminal Court said the pardon granted to Fujimori in a human rights case for which he was serving a 25-year sentence did not apply to the murders of the group.
Prosecutors asked to try the ex-president and 22 others for the death squad killings.
Fujimori, 79, was pardoned by the current Peruvian president, Pedro Pablo Kuczynski, on December 24 on humanitarian grounds because of ill health.
The pardon triggered street protests in Peru and was slammed by international rights groups as a blow in the struggle against impunity.
Kuczynskis pardon was seen by many as quid pro quo for help from Fujimoris lawmaker son Kenji days earlier in beating an impeachment vote in Congress over alleged corruption.
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