"The prosecution's evidence ... will reveal that over 200 children, women, elderly and civilian men were killed in an attack during which women were sexually enslaved in camps and repeatedly raped," Fatou Bensouda, the court's deputy prosecutor, said on Friday.
The alleged attack took place in the village of Bogoro in the northeastern district of Ituri, a conflict zone rich in natural resources including gold, diamonds and oil, in February 2003.
Bensouda told a panel of three judges that villagers awoke to the sound of gunfire on the morning of the attack.
"With calculated precision, over 1,000 soldiers ... under the command of Germain Katanga and Mathieu Ngudjolo Chui entered the village with one communicated and agreed goal: to erase the village of Bogoro."
Bensouda said the soldiers burnt several houses, sometimes with the inhabitants still inside.
"Many civilians were killed, either by bullet or knife, or were captured, sexually enslaved or otherwise," the deputy prosecutor said.
"Civilians were detained in a room full of dead bodies. The next day, the militias forced those people to lure other civilians out of their hiding places in order for the militia to kill them."
The case is the second to be brought before the ICC, the world's first permanent international criminal tribunal.
The first, of another Congolese militia leader, Thomas Lubanga, has been halted over concerns that evidence was withheld from the defence and he could therefore be denied a fair trial.
Defence lawyers have asked the judges to also suspend the case against Katanga and Ngudjolo as the prosecution is using the same evidence.
However the court has decided to go ahead with the hearing, as the proceedings are not as advanced.
A "confirmation of charges" is being presented by the prosecution to the judges in order to support the charges against Katanga and Ngudjolo.
This process will last several weeks and the court will then have 60 days to decide whether or not to go to trial.
The Ituri conflict, which began after a peace accord officially ended Congo's 1998-2003 war, turned members from the Hema and Lendu ethnic groups against one another.
Katanga, also known as "Simba" or lion, headed the Patriotic Forces of Resistance of Ituri (FRPI), while Ngudjolo led the allied Front of Nationalists and Integrationists (FPI) forces.
Luis Moreno-Ocampo, chief prosecutor, said he hoped that the cases would help to heal the situation in Ituri.
"Perpetrators will be held accountable ... the work of justice can help Ituri move forward," he said in a statement.
The ICC is also investigating war crimes in Sudan's Darfur region, Uganda and the Central African Republic.