The boat sank as it was crossing the Helmand River, which snakes through southern Helmand province, the world's leading opium poppy region and site of fierce battles the last several months. Hundreds of Taliban insurgents are believed to be in Helmand.
The Afghan army was investigating to see how many Taliban insurgents and civilians were on board, the Defense Ministry said in a statement. It did not say what caused the boat to sink.
A ministry spokesman, Gen. Zahir Azimi, said that Afghan troops saw the boat sink from a military helicopter, suggesting that those on the boat may have been involved in a battle.
Meanwhile, 34 suspected Taliban fighters were killed in gunbattles over the past two days in Helmand province's Kajaki district, near where a U.S. helicopter went down on Thursday. The crash killed five Americans, a Canadian and a Briton.
An Interior Ministry statement said four Taliban group commanders were among the 34 killed. The Defense Ministry said two Afghan soldiers were killed and two wounded in the operations.
Suspected Taliban militants also attacked a local police commander's home Saturday, killing five of his family members and sparking a gunbattle with police that left 10 insurgents dead, an official said.
The attack in the southeastern province of Ghazni killed the commander's wife, two sons and two nephews, said Interior Ministry spokesman Zemeri Bashary. The commander worked for Afghanistan's auxiliary police, a system of backup officers who supplement the country's regular police force.
The attack came a day after Taliban fighters targeted the home of a police official in the eastern province of Paktia. That assault led to a gunfight which left six insurgents dead.
Taliban militants often target police and government officials. More than 1,900 people have been killed in insurgency-related violence in Afghanistan this year, according to an Associated Press count based on U.S., NATO and Afghan officials.
At a rally in Pakistan, meanwhile, a man described as the Taliban's new top field commander vowed in an audiotaped message to liberate Afghanistan from "American slavery," said Abdul Sattar Chishti, the cleric who organized the event.
Chishti said more than 12,000 people listened to the speech by the brother of Mullah Dadullah, the top Taliban commander who was killed in a U.S. operation last month in southern Afghanistan.
He said Dadullah Mansoor vowed to avenge his brother's death and those of others killed while fighting U.S., NATO and Afghan forces.
"The blood of my brother will never go waste. We will never forget his sacrifices, and the role of other martyrs. We will complete Dadullah's mission by expelling Americans and liberating Afghanistan," Chishti quoted Mansoor as saying.
Although pro-Taliban elders have held similar rallies in northwestern tribal regions, protests the size of the one organized in Killi Nalai are rare.