Army spokesman Philip Aguer told AFP news agency on Tuesday that the boat had been overloaded with people trying to escape the violence.
“The reports we have are of between 200 to 300 people, including women and children,” he said.
“They all drowned. They were fleeing the fighting that broke out again in Malakal.”
Meanwhile, battles raged in several cities in South Sudan on Tuesday.
Heavy fighting was reported in Malakal, the capital of oil-producing Upper Nile state, as rebel forces staged a fresh attack to seize the town.
Control of Malakal 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.
The army reported heavy fighting south of Bor, as the government sought to retake the town from rebels, the largest in their control.
“We are marching on Bor, there was very heavy fighting late on Monday,” Aguer said.
However, he rejected rebel claims to have captured the river port of Mongalla, situated between Bor and the capital Juba.
“We are north of Mongalla, we remain in full control there,” Aguer said.
According to the United Nations, some 400,000 civilians have fled their homes over the past month.
The fighting is between South Sudan’s President Salva Kiir and his former deputy Riek Machar.