Moreno-Ocampo's report calls for the UN Security Council to demand that Sudan's government hand over two Sudanese men who have been indicted by the ICC on charges of crimes against humanity.
One is Ahmed Harun, Sudan's humanitarian affairs minister, who is accused of organising a system to recruit, fund and arm janjawid militias to support the Sudanese military.
The other is Ali Kushayb, known as a "colonel of colonels" among the janjawid.
The report comes as UN Security Council ambassadors arrived in Khartoum to hold talks with Sudanese government officials.
The UN delegation is in the country on a three-day visit to help save a 2005 peace agreement that brought an end to a 20-year civil war.
In recent weeks there has been fierce fightingin the oil-rich region of Abyei between northern government soldiers and former southern rebels of the Sudan People's Liberation Army.
A spokeswoman for the ICC said on Tuesday that the ICC chief prosecutor's report is the first instance where the entire Sudanese government has been linked to abuses in Darfur.
The atrocities include killing, torture and the rape of civilians including girls as young as five or six while their parents are forced to watch, Moreno-Ocampo's report says.
It also says senior Sudanese officials are linked to the burning and looting of homes, bombing of schools and destroying of mosques.
Human rights groups and others have long accused Sudan's government of arming Arab militias, known as janjawid, that have allegedly attacked Darfur villages.
Sudanese leaders have denied any links to janjawid militias.
The report does not identify any officials or present evidence of specific crimes.
Moreno-Ocampo will name names and present evidence next month at a pre-trial hearing by three of the court's judges at The Hague, Florence Olara, a spokeswoman for the ICC, said.
Prosecutors have been investigating the alleged abuses for some time from a field office in neighbouring Chad, which borders Darfur.
Moreno-Ocampo has said in a past report that investigators collected evidence from more than 100 witnesses in 18 countries.
The conflict in Darfur began in early 2003 when rebels took up arms against the government.
Hundreds of thousands of people have died in ensuing violence and millions more have been forced from their homes.
The use of janjawid militias to commit crimes, and then characterising them as "autonomous bandits or self-defence militia" is "part of the cover-up", Moreno-Ocampo's report says.
There is evidence of a criminal plan based on the mobilisation of the armed forces, the intelligence services, the diplomatic and public information bureaucracies and the justice system, it says.