“The reports we have are of between 200 to 300 people, including women and children. The boat was overloaded,” said army spokesman Philip Aguer.
“They all drowned. They were fleeing the fighting that broke out again in Malakal.”
The country has been rocked over the past three weeks by fierce fighting between government forces and those loyal to his sacked deputy Riek Machar.
More than 1,000 people have been killed, while 230,000 have been from their homes.
The clashes have continued despite stuttering peace talks in neighbbouring Ethiopia.