Chester Stamp, prosecuting before the International Criminal Tribunal in the former Yugoslavia, stressed Djordjevic's role in operations carried out against ethnic Albanians, including the expulson by the Yugoslavian and Serbian armies of a third of the Albanians living in Kosovo.
Stamp told the court in the Netherlands that ethnic Albanians were forced to leave their homes, with the women and children separated from the men, who were then killed.
He said the bodies were concealed by being moved to mass graves in Serbia.
A court indictment alleges that Djordjevic "willingly participated in a joint criminal enterprise whose aim was to expel the majority of the Kosovo Albanian population to ensure continued Serbian control over the territory".
It said that forces involved in the operation were also "alleged to have sexually assaulted women, as well as looted and destroyed civilian property and religious sites".
On Tuesday, Djordjevic told the court that the operations he oversaw were not aimed against civilians but the "terrorists" of the Kosovo Liberation Army, who were seeking the secession of Kosovo from Yugoslavia.
"They wanted to secede and created the semblance of a humanitarian catastrophe for which Serbia would be blamed," he said.
Djordjevic, who was an aide to Slobodan Milosevic, the former Yugoslav president, was arrested in Montenegro in June 2007 after nearly four years on the run.