The convoy was being guarded by 150 soldiers from South Sudan's army
North Sudan has been accused of providing arms that were used to attack barges carrying UN food aid on Sunday.
A governing party leader in South Sudan told the BBC arms were being distributed in the south to spread dissent between rival groups.
He said Khartoum wanted to destabilise the region before a referendum on southern independence due in 2011.
On Sunday, 27 barges were attacked and looted by gunmen to stop emergency food aid reaching a rival group.
A 22-year war between the mainly Muslim north and the Christian and animist south ended in 2005, after 1.5 million people died.
Pagan Amum, secretary general of the Sudan People's Liberation Movement, told the BBC's Focus on Africa programme the spirit of the comprehensive peace agreement which ended the fighting had been "assassinated" by Khartoum, as he accused its government of distributing arms in the south.
Gunmen from the Jikany Nuer ethnic group launched Sunday's assault on the flotilla near the town of Nasir, close to Sudan's eastern border with Ethiopia.
The barges, carrying 700 tonnes of supplies, were travelling to the town of Akobo when they were set upon; 16 of the vessels made it back to Nasir.
The convoy was being guarded by 150 soldiers from South Sudan's army.
Local sources suggest around 40 people are feared dead from the attack, but the figures cannot be verified.
Several hundred people have been killed in clashes between rival ethnic groups, including the Jikany Nuer, in the south in recent months.
Under the 2005 peace deal the former rebel SPLM formed a power-sharing government with President Omar al-Bashir's National Congress Party in Khartoum.
But relations between the former foes are tense, with national elections due in 2010 and then a referendum on whether the south should secede in 2011.