John Garang, chairman of the Sudan People's Liberation Movement (SPLM), told Annan at Rumbeik on Sunday that more than a quarter-million refugees had returned to homes around this former rebel stronghold since the signing of the January peace agreement with the Sudanese government in Khartoum.
Now, Garang said, the war-ravaged region needed help feeding the returnees, who had not yet been able to go back to farming.
"The UN food pipeline is empty," Garang told Annan.
The UN secretary-general spent about five hours in southern Sudan in the last stop on his three-day tour of Sudan before flying to Addis Ababa, Ethiopia.
He was greeted at the airport there by hundreds of colourfully dressed locals who danced and shouted greetings to the secretary-general.
White bulls gifted
Farmers presented a pair of white bulls to Annan and asked the UN leader to lay his hands on them in a good luck gesture.
Enthusiastic well-wishers lined the roads to greet Annan as his motorcade passed.
The Sudan News Agency quoted Annan as saying that his visit to Rumbeik was to show "backing for the peace process in the Sudan".
Annan visited refugee camps in
Darfur as well as south Sudan
January's peace deal signed in Kenya made Garang a first vice president, cleared the way for the drafting of a new constitution, and gave southern states the opportunity to vote on secession in six years.
The SPLM also will take 30% of seats in a transitional national government.
The 21-year war pitted the Arab Muslim-dominated government in Khartoum against rebels fighting for greater autonomy and a larger share of the country's wealth in the largely African animist and Christian south.
Separately, Sudan's First Vice-President Ali Osman Mohamed Taha has called on rebel groups in Sudan's western Darfur to join peace talks in Nigeria on 10 June, aimed at ending war in the troubled region.