The U.N. secretary-general flew into rain-soaked Khartoum to be greeted by about 200 women protesting on the airport tarmac against a Security Council resolution referring alleged war crimes in Darfur to an international court.
During his three-day visit, he will hold talks with Sudan's leadership and go to Darfur to view African Union monitors working to defuse violence that has killed tens of thousands and forced 2 million people from their homes.
About 2,300 troops from African Union member states such as South Africa, Rwanda, Gabon, Nigeria and Senegal and hundreds of civilian police are monitoring a shaky ceasefire between Khartoum and rebel groups in Darfur.
Annan said he was pleased with the decision by international donors to give nearly $300 million to fund a larger AU force to help restore stability to the troubled region, after a meeting in the Ethiopian capital Addis Ababa that ended on Thursday.
U.N. officials estimate about 180,000 people have died in Darfur through violence, hunger and disease since the rebels took up arms against the Arab-dominated government in February 2003, complaining of neglect.
Annan first visited Sudan 11 months ago, at the height of the humanitarian crisis in Darfur. Since then the situation in the refugee camps has improved, but security remains a problem for almost 10,000 aid workers delivering food and medicine.
"We discussed the need for us to do everything we can to bring security to Darfur and to ensure that the farmers can go back to their land and plant and cultivate and harvest their crops," Annan told reporters after an hour-long meeting with Sudan's foreign minister, Mustafa Osman Ismail.
"Otherwise, we are going to have a major humanitarian effort which will stretch the capacities of the international community."
Annan will travel on Saturday to South Darfur, the state which has seen some of the worst violence in recent months and where aid workers complain most of harassment by local authorities.
He said the rebels also and had to respect the ceasefire and allow aid workers more access to their areas.
He also noted that donor countries had switched their attention from southern Sudan, where rebels signed a peace deal in January with the government to end more than two decades of civil war, to Darfur in the west.
"It is a shame that in the south we have a peace agreement but we don't have the resources required," he said. "We should not allow the peace agreement to get into trouble for lack of money."
He will meet former rebel John Garang, the head of the former southern rebel Sudan People's Liberation Movement, in his base in Rumbek on Sunday.