The assailants attacked the boat on a waterway that connects the northern regions of Gao and Mopti during the rainy season, and raided the camp in the Bourem Circle, in Gao region.
A resident and local official said the boat was transporting soldiers.
Around 50 assailants were killed in subsequent fighting, the interim government said.
The government said insurgents from a West African branch of Al-Qaeda, called Jama’at Nusrat al-Islam wal Muslimeen (JNIM), had claimed responsibility for the attacks, which Reuters could not immediately confirm.
Mali is one of several West African countries battling a violent insurgency with links to Al-Qaeda and Islamic State that took root in Mali’s arid north in 2012 before spreading across the region.
Frustrations about growing insecurity have spurred military coups in the three worst-hit countries – Mali, Burkina Faso, and Niger – since 2020, worrying global powers with strategic interests in the region.
Attacks have worsened in Mali since the military seized power in two coups in 2020 and 2021, kicked out French forces and a United Nations peacekeeping mission, and teamed up with Russian private military contractor Wagner Group.
The UN, which is in the process of departing, has handed over a series of northern bases to the army.
Islamist groups have filled the void left by the departure of thousands of blue helmets and French soldiers in the north and east.
The boat that was attacked was travelling from the city of Gao when it was hit. The operator, Comanav, usually transports residents and supplies on its boats.
But a Gao resident and a local official, who did not want to be named for security reasons, said today that it had also been transporting military personnel before yesterday’s attack.
“We thought that if the jihadists learned that there were soldiers on board, they would attack, and that’s what happened,” the resident told Reuters.
The official said that the boat was going to the city of Timbuktu, which has been under a JNIM-imposed blockade since last month, creating food and aid shortages.
The attack on the army base occurred about 230km north of Gao, a city which for years has been surrounded by violent assaults.
“In Gao, the anxiety of local residents is palpable as threats of attacks mount. Some nomadic families have been leaving the town recently, which is a sign that something is up,” the resident said.