"Darfur is a very important and sensitive case that should be dealt with in full coordination with the African Union," Amr Mousa said in Khartoum.
Mousa said he discussed with Omar al-Bashir, Sudan's president, developments in the region.
He has said Darfur will be on the agenda at the Arab summit that opens in the Sudanese capital on Tuesday.
Meanwhile, the UN Security Council agreed on Thursday to ask Secretary-General Kofi Annan to expedite planning for a new UN force in Darfur.
The text of a draft resolution, put forward by Washington and set to be adopted by the 15-nation council on Friday, will give Annan until April 24 to prepare "a range of options for a United Nations operation in Darfur,'' according to a copy obtained by Reuters.
It will also ask the UN leader to prepare recommendations within a month on how a separate UN peacekeeping mission in southern Sudan could help stop Uganda's notorious Lord's Resistance Army, an armed group that has wreaked havoc in the region for decades.
The LRA has terrorised communities in Uganda's remote north for two decades, and some of its fighters have recently crossed over into neighbouring Democratic Republic of Congo and Sudan.
Led by self-proclaimed prophet Joseph Kony, the LRA has killed tens of thousands of unarmed villagers, slicing off survivors' lips or ears and abducting more than 10,000 children as fighters, porters and sex slaves.
An African Union peacekeeping force of about 7,000 troops is already in Darfur, seeking to protect villagers from marauding Arab militias that the United Nations and the United States say are being armed by the Khartoum government - an allegation the Sudanese government denies.
But the poorly equipped and under-financed AU force has proven ineffective in ending the violence, prompting Annan to call for its replacement by a bigger UN force.
Sudan's government, however, has said it does not want UN troops in Darfur until a peace agreement is reached in talks taking place in the Nigerian capital Abuja.
The AU's Peace and Security Council, bending under pressure from Sudan, voted this month to extend its mission in Darfur till September 30 while affirming in principle its plan to eventually hand over to a UN force.
US Ambassador John Bolton said this week he wanted the new resolution to accelerate planning and lay the groundwork for a smooth transition to a UN force in Darfur without waiting for formal approval from the AU and Sudan.
The text will also extend the mandate of the UN peacekeeping mission in the south, due to expire on Friday.