In a report to the UN Security Council, Luis Moreno-Ocampo said the office had documented "thousands of alleged direct killings of civilians by parties to the conflict," including "a significant number of large-scale massacres, with hundreds of victims in each incident."
Mr Ocampo told the council that his office was investigating allegations that some of the groups implicated in the crimes in Darfur "did so with specific genocidal intent".
He said identifying those with the greatest responsibility for the most serious crimes in Darfur was a key challenge for his probe. But said he would not draw any conclusions pending the completion of a "full and impartial investigation".
Mr Ocampo said interviews of victims and witnesses reported that men perceived to be from the Fur, Massalit and Zaghawa ethnic groups were "deliberately targeted."
Evidence cited eyewitness accounts that "the perpetrators made statements reinforcing the targeted nature of the attacks, such as 'we will kill all the black' and 'we will drive you out of this land'."
The report also said there had been a "significant amount of information indicating that thousands of civilians have died since 2003” as a result of lack of shelter and basic necessities for survival after their homes and food stocks were destroyed and their property looted.
Mr Ocampo's office also recorded "hundreds of alleged cases of rape", which the report said was indicative of an endemic practice among some groups involved in the conflict.
It highlighted a "widespread pattern of displacement of civilians, with recent estimates of some two million displaced persons and refugees from Darfur.
The study covering the October 2002-May 2006 period, also referred to continued reports of direct attacks on humanitarian workers and peacekeepers, including the killing of African Union peacekeepers in 2005 and 2006.
The ICC, based in The Hague, is mandated to try genocide, crimes against humanity and war crimes. It can also try crimes of aggression although member states have not yet agreed on the legal definition for such crimes.