He is alleged to have led an army hit squad known as the Colina Group, which has been blamed for the massacres carried out during the government's 20-year civil conflict with Maoist rebels.
The former leader has also denied waging a "dirty war' against Peru's left-wing
Brutal civil war
Montesinos, 63, has also denied the charges and says the army instead are guilty of the massacres, while in other cases pending against him he has claimed he was acting on Fujimori's orders.
He is currently serving a 20-year prison sentence for trafficking arms and for corruption.
Lucia Newman, Al Jazeera's Latin American editor, said it was not surprising that
Montesinos - due to face trial himself over the killings - did not implicate his former boss, as it would have been tantamount to implicating himself.
Fujimori fled to exile in Japan after his removal in 2000 following a corruption scandal which involved Montesinos.
He was held in Chile during a visit to the country in 2005 and extradited to Peru in September 2007 on charges of involvement in ordering killings and kidnappings during his time as leader.
Peru's civil war between the government and various Maoist rebel groups, most notably the Shining Path, is estimated to have left at least 70,000 dead.