"The reports we have are of between 200 to 300 people, including women and children. The boat was overloaded," army spokesman Philip Aguer said."They all drowned. They were fleeing the fighting that broke out again in Malakal."
Violence broke out in South Sudan on December 15 and quickly spread across the country, often in ethnic-based attacks. A precise death toll is not known, but the International Crisis Group has estimated that nearly 10,000 people have died. The UN says nearly 400,000 people have fled their homes.
On Tuesday, fighting continued up and down the Nile, AFP reported.
Heavy fighting was reported in Malakal, the state capital of oil-producing Upper Nile state in the north. Rebel forces staged a fresh attack to seize the town, which has already changed hands twice since the conflict in South Sudan began on December 15.
"There is fighting anew in and around Malakal," United Nations aid chief for South Sudan Toby Lanzer said, adding that the peacekeeping base had been swamped with almost double the number of people seeking shelter, rising from 10,000 to 19,000.
Heavy fighting reported further south near Bor, as the government sought to retake the town from rebels, the largest in their control.