The distribution was the first in the area since the signing of the southern peace agreement in January between the Sudanese government and the southern Sudan People's Liberation Movement/Army (SPLM/A).
While the cross-line distribution got off to a successful start, it came to a standstill in Upper Nile State when the local commissioner of New Fanjak, who is also a pro-government militia leader, insisted that the food assistance was insufficient and on 17 May demanded a double ration for his area.
"This was a test case to open the way for future cross-line missions, the beginning of more regular access and cooperation between north and south," Hans Vikoler of the UN World Food Programme (WFP) and leader of the inter-agency mission said.
After two days of negotiation, aid workers turned back with the food and other items, such as children's books, fishing hooks and seeds and farming tools, which were intended to be delivered ahead of the planting season.
Vikoler said continuing the distribution to other towns along the Nile corridor could inflame tensions and provoke potential violence.
"The last time we did a distribution was in October 2004, and it was to government areas only," Vikoler added. "Now the context has changed. With this exercise we target the whole population without distinction. We are in peace and we will come back regularly, but some in the population have doubts."
The area along the White Nile in Upper Nile State was the scene of armed conflict in 2004. Many armed militias have not been integrated into government or SPLM/A forces, and conflicts that occasionally flare up over resources and cattle are aggravated by the availability of firearms in the region.
The five-day inter-agency assessment mission in February found that there was a significant food gap as well as need for agricultural inputs ahead of the planting season, aid workers said.
Armed clashes in 2004 kept populations on the move, preventing them from planting crops. Lack of rainfall exacerbated the poor harvest. The report also noted that there was a shortage of boreholes for clean water and that education and health facilities were understaffed or had been destroyed in the fighting.
Since October 2004, New Fanjak's population had doubled to nearly 6,000. The increase was the result of people returning home after the signing of the peace agreement and newly displaced people seeking refuge in town because of insecurity in the surrounding areas.
Although there were significant needs, there were other issues than just food security at stake, aid workers observed. The distribution was aimed as proving that the barriers and regulations that restricted people's movements in this formerly war-torn country were coming down.
"The food is symbolic," Hans Vikoler noted. "This cross-line distribution is part of a larger effort to facilitate returns and bring a message of joint cooperation and action."
Using river barges was a practical and affordable way to bring assistance to these communities in a sustainable way until they got back on their feet, he added. Large amounts of supplies and personnel could be moved by barge at a significantly lower cost compared to air transport.
To date, transporting aid supplies to war-affected populations in southern Sudan had been one of the world's most costly relief operations because of insecurity, long distances and lack of infrastructure.
With the opening up of more river and road corridors, aid agencies are hoping this will change.
The war between the SPLM/A and the Sudanese government in the south erupted in 1983 when rebels took up arms against authorities based in the north to demand greater autonomy. The fighting has killed at least two million people, uprooted four million more, and forced some 550,000 to flee to neighbouring countries.