Djordjevic, 60, who headed the Serbian Interior Ministry's Public Security Service, is accused of "taking part in a widespread campaign of terror and violence directed at ethnic Albanian civilians of Kosovo in 1999," the International Criminal Tribunal for the former Yugoslavia (ICTY) said in a statement.
Djordjevic, who also served as a deputy interior minister, allegedly took part in an operation to expel Kosovo Albanians and establish Serbian control over the province.
"This was to be achieved by a systematic campaign of murders, deportations, forcible transfers and persecutions directed at the Kosovo Albanians," the tribunal said, adding that hundreds of people were killed and around 800,000 Kosovo Albanians deported as a result.
Serbian forces, including police units allegedly commanded by Djordjevic, "sexually assaulted women, as well as looted and destroyed civilian property and religious sites."
The former official pleaded not guilty to all charges.
Djordjevic remained in his post after the fall of the Milosevic regime on October 2000, but disappeared immediately after the bodies of Kosovo civilians were discovered in a mass grave. Djordjevic is thought to have played a key role in hiding the bodies.
He was arrested on June 17, 2007 in Montenegro after almost four years on the run and extradited to The Hague.
Since its establishment 15 years ago the ICTY has indicted 161 people for war crimes committed on the territory of the former Yugoslavia.
