The court also added three counts of crimes against humanity and four counts of war crimes to the arrest warrant of Gen Ntaganda - known as the "Terminator".
Forces loyal to him are currently threatening eastern DR Congo's biggest city, Goma.
They defected from the army in April, after pressure grew on the Congolese government to arrest him when a former comrade, Thomas Lubanga, became the first person to be convicted of war crimes by the ICC.
"There are reasonable grounds to believe that Bosco Ntaganda is responsible for three counts of crimes against humanity, consisting in murder, rape and sexual slavery, and persecution," the court said in a statement."Bosco Ntaganda allegedly bears individual criminal responsibility for four counts of war crimes consisting of murder, attacks against the civilian population, rape and sexual slavery, and pillaging," it added.
He was first indicted in 2006 by the ICC for allegedly recruiting child soldiers for the same rebel group as Lubanga.
The new charges, allegedly committed in the Kivus in 2002-2003, came about as a result of evidence given during the Lubanga trial.
Analysts say arresting either men will be difficult since their whereabouts are unknown, with Gen Ntaganda, a Tutsi, leaving his Goma base in eastern DR Congo just as soldiers loyal to him deserted the Congolese army.
The renegade general denies masterminding the mutiny by former members of the CNDP rebel group, whose fighters were integrated into the Congolese army as part of a peace deal three years ago.
The Congolese government has refused to hand over Gen Ntaganda, saying that it now wants to put him on trial in the country for his role in the latest fighting.