He is accused of crimes against humanity and war crimes for murders, inhuman acts, attacks on villages, plundering, sexual slavery and conscription of children committed between July 2002 and the end of 2003.
Ngundjolo allegedlly targeted the attack of the Bongolo village.
He is the third accused held in the prison of Scheveningen, a suburb of The Hague.
Thomas Lubanga, leader of the Union of Patriotic Congolese (UPC), has been in custody for more than two years.
The opening of his trial, which looks already to be a watershed trial with an announced duration of eighteen months, is scheduled for 31 March.
Germain Katanga, former Chief of Staff of the Front for Patriotic Resistance of Ituri (FPRI), allied with the FNI, could be on trial alongside Ngundjolo.
The Prosecutor. Luis Moreno Ocampo, said via live satellite from Bangui, in the Central African Republic; where after the DRC, Uganda, and Darfur, the prosecution opened its fourth investigation, targeting "the crimes committed by Laurent Nkunda [the National Council for the Defence of the People], the FDLR [Democratic Liberation Forces of Rwanda, Hutu extremists] and the regular army".
The prosecutor promised to issue new warrants, welcoming the fact that "the act of engagement of Goma [peace agreement signed on 23 January 2008] reaffirmed the Principle of impunity by excluding these crimes from the field of considered amnesty".
Luis Moreno Ocampo also specified that his investigations are tracking" individuals who could have played a part in the support of the armed groups".
© Hirondelle News Agency