Sudanese Foreign Minister Mustafa Osman Ismail briefed Zoellick on the obstacles to ending the two-year Darfur crisis, according to the official Sudan News Agency (SUNA).
Ismail told Zoellick that "it is unjust" to attribute all that happened in Darfur to the Sudanese government.
The foreign minister said the Darfur rebels should also be blamed for their failure to observe a ceasefire.
Ismail urged the United States and the international community to press the Darfur rebel groups to meet their commitments.
The two sides also discussed the implementation of the North- South peace deal that the Sudanese government and the Sudan People's Liberation Movement (SPLM) signed in January ending a 21- year civil war.
Sudanese Charge D'affaires in Washington Khidir Haroun told reporters after the meeting that Zoellick promised to seriously review the Darfur situation and to urge rebels to fulfill their pledges to end the conflict.
Zoellick arrived in Khartoum Thursday on a two-day visit to Sudan.
Rebels in Darfur took up arms against the government in February 2003, accusing it of neglecting the barren area. Tens of thousands of people have been killed in the fighting in Darfur and more than 2 million have fled their homes to makeshift camps in the remote, western desert region.
Washington has called the atrocities in Darfur as genocide, a charge Khartoum rejects.
Peace talks under the auspices of the African Union between the Sudanese government and the two main Darfur rebel groups collapsed last year in the Nigerian capital Abuja.