The report of an imminent attack was later found to be false, China's official Xinhua news agency reported Monday.
Upper Nile State information minister Philip Jiben said the deaths occurred when a boat carrying people from the town of Malakal sank. Jiben said only two children were rescued.
He said the people had fled the town after receiving reports the forces of former vice president Riek Machar were going to attack.
"No attack was launched against Malakal," Jiben said. "The town is completely calm and the life is progressing naturally. There is no any fighting at any part of the town."
Machar is engaged in a conflict with the forces of South Sudan President Salva Kiir Mayardit. The two sides are meeting in Ethiopia to negotiate a ceasefire.