Prosecutors said Ntaganda was central to the planning and operations for the Union of Congolese Patriots rebels and its military wing, the Patriotic Forces for the Liberation of Congo (FPLC).
The FPLC killed at least 800 people as it fought rival militias in Ituri, prosecutors said.
In one attack directed by Ntaganda, judges said that soldiers killed at least 49 captured people in a banana field behind a village using "sticks and batons as well as knives and machetes."
"Men, women and children and babies were found in the field. Some bodies were found naked, some had hands tied up, some had their heads crushed. Several bodies were disembowelled or otherwise mutilated," Fremr said.
Formerly a Congolese army general, Ntaganda then became a founding member of the M23 rebel group, which was eventually defeated by Congolese government forces in 2013.
The first-ever suspect to voluntarily surrender to the ICC, he walked into the US embassy in the Rwandan capital Kigali in 2013 and asked to be sent to the court, based in the Netherlands.
Ntaganda is one of five Congolese warlords brought before the ICC, which was set up in 2002 as an independent international body to prosecute those accused of the world's worst crimes.
Ntaganda's former FPLC commander Thomas Lubanga was sentenced to 14 years in jail in 2012.
But it has suffered a string of setbacks over recent years with some of its most high-profile suspects walking free, including Ivorian former leader Laurent Gbagbo earlier this year.
It has also been criticised for mainly trying African suspects so far.
The US administration of President Donald Trump has also attacked the court after warning it against prosecuting US service members over war crimes in Afghanistan.
In a separate hearing on Monday, judges are to determine whether there is enough evidence for a Malian jihadist to face trial for demolishing Timbuktu's fabled shrines, as well as for rape, torture and sex slavery.
Al Hassan Ag Abdoul Aziz Ag Mohamed Ag Mahmoud was captured and transferred to the court last year.