During a short hearing before Presiding judge Dennis Byron, the prosecution read an amended indictment which adds 18 factual allegations to the charges of genocide, war crimes, crimes against humanity, and rapes perpetrated by his men.
"I plead not guilty", the accused answered quietly after the new indictment was read.
The trial should not start before July.
Nizeyimana is notably prosecuted for several murders of Tutsis, including the assassination of Rosalie Gicanda, the widow of the next to last king of Rwanda, Mutara III Rudahigwa.
The indictment further alleges that Nizeyimana participated in the drawing up of lists of Tutsi intellectuals to be killed, and highlights that the Captain was "a member of President Habyarimana‘s inner circle".
It goes on charging Nizeyimana with letting his men rape Tutsi girls and women, as part of a genocidal project.
The ICTR is the first international court to have adopted a jurisprudence positing that rapes can be constituent elements of a collective plan to eliminate in part or in whole a racial or ethnic group.
Nizeyimana, 46, was second in command of the Noncommissioned Officers School (Ecole des sous-officiers, ESO) in the southern town of Butare at the time of the genocide.
He was arrested in Kampala (Uganda) on October 5 and transferred to the UN Detention facility in Arusha (Tanzania).
He ran a small business in Goma (eastern Democratic Republic of the Congo, DRC) before his arrest. Knowing he was wanted by the ICTR, he frequently changed his identity. He entered Uganda under the false name of Hitimana Kabogo.
Nizeyimana was on a list of ICTR's twelve most wanted fugitives.
© Hirondelle News Agency