The ICC named Humanitarian Affairs Minister Ahmed Haroun and Janjaweed militia leader Ali Muhammad Ali Abd al-Rahman, also known as Ali Kushayb.
Some 200,000 people have died in a four-year conflict in
'Rape and torture'
The two men are suspected of 51 counts of war crimes and crimes against humanity, ICC chief prosecutor Luis Moreno-Ocampo said.
They include crimes committed during attacks on villages near Kodoom, Bindisi, Mukjar and Arawala in
Sudanese Justice Minister Mohammed Ali al-Mardi said: "We are not concerned with, nor do we accept, what the International Criminal Court prosecutor has opted for."
He added: "All the evidence the prosecutor referred to is lies given to him by people who bear arms against the state, bear arms against citizens and kill innocent citizens in
The BBC's Jonah Fisher in
According to ICC prosecutors, he commanded thousands of men and ordered them to rape, torture and kill the local population.
But our correspondent says it is the naming of Ahmed Haroun that will have wider repercussions.
Mr Haroun had responsibility for
'Criminal responsibility'
Mr Moreno-Ocampo asked judges to issue summonses for the two men, saying there was reason to believe they bore "criminal responsibility for crimes against humanity and war crimes committed in Darfur in 2003 and 2004".
The attackers, he said, "did not target any rebel presence. Rather they targeted civilian residents based on the rationale that they were supporters of the rebel forces".
The strategy, Mr Moreno-Ocampo added, "became the justification for the mass murder, summary execution and mass rape of civilians who were known not to be participant in any armed conflict".
He said: "Ahmad Haroun visited Darfur on a regular basis and became known to people in Darfur as the official from
"The evidence shows that Ahmad Haroun provided arms for the Janjaweed from a budget that was unlimited and not publicly audited."
After Mr Moreno-Ocampo has filed the evidence of alleged war crimes with the court, its judges will have to decide whether to open an inquiry against the suspects with the aim of issuing international arrest warrants.
UN Human Rights Commissioner Louise Arbour said she hoped Tuesday's developments would be a "strong deterrent" against more bloodshed.
She said she expected more charges to be brought against both government and rebel officials.
"remained about the North's intentions, but added that "so far, the indications were in a positive direction".
Photo caption
Sudanese displaced from