Lam Akol, a senior politician in the rebel Sudan People's Liberation Army (SPLA), claimed on Tuesday that government-sponsored militiamen had torched villages in the Shilluk Kingdom.
He added that thousands had also been displaced and that at least 36 were killed in March alone.
The United Nations estimates that up to 50,000 people have been driven from their homes in Shilluk since fighting began in March.
The area is meant to be covered by a ceasefire in a decades-old war in southern Sudan that ought to end in the next few weeks as the government and the SPLA conclude a peace deal.
Diplomats say the violations of the truce in Shilluk since March show how difficult it could be to implement any eventual peace deal in the south.
"It was the strategy of the government militias not only to burn the food crops but to torch the grass used in building huts," Akol told a news conference on a visit to Nairobi. He said water lilies were the only edible plant left in the area.
"The condition of these displaced persons is miserable. They are staying in an area infested by mosquitoes."
Children who have escaped the
fighting enjoy first meal in days
UN and non-governmental groups in a consortium of relief organisations known as Operation Lifeline Sudan have been forced to suspend operations and relocate staff several times this year due to the conflict in the Shilluk kingdom.
The violence pits the army and militiamen loyal to the government in Khartoum against the SPLA, which has been fighting for greater autonomy from the government for over 20 years.
Akol said the SPLA had wrested control of the Shilluk areas of Papwojo chieftaincy, Fangak and Bahr al-Jabal from government-backed militias this month, and he urged the UN and other relief groups to return to those places.
Political tensions worsened in Shilluk last October when Lam Akol angered some supporters by merging his Sudan People's Liberation Army-United with the much larger main southern rebel movement, John Garang's SPLA, more than 10 years after leaving.
Akol spent part of the 1990s as a government minister and part as a politician opposed to both Khartoum and the SPLA.
The conflict is separate from one in the westerly Darfur region, where more than 100,000 have been displaced and UN investigators have accused Sudanese troops and militias of massive human rights violations.