The attack comes after an Al Qaeda-linked alliance announced last month it was blockading Timbuktu, the historic crossroads city of northern Mali.
Attacks on an army base and a passenger boat on the Niger River in northern Mali on Thursday by suspected militias killed 64 people, a Malian official said.
The two separate attacks targeted the Timbuktu boat on the Niger river and an army position at Bamba, in the northern Gao region with "a provisional toll of 49 civilians and 15 soldiers killed", according to a government statement.
It did not specify how many died in each assault, but the assaults were "claimed" by a group affiliated to Al Qaeda.
Earlier, the Malian army said on social media that the boat was attacked around 1100 GMT by "armed terrorist groups".
"The vessel, plying an established route between cities along the river, was targeted by at least three rockets which aimed at its engines," the operator Comanav said separately.
"The vessel was immobilised on the river and the army are evacuating passengers," a Comanav official said, speaking on condition of anonymity.
Images on social media showed a cloud of black smoke rising above the river. The incident took place in a remote area and the images could not be verified independently.
The Niger is a vital transport link in a region where road infrastructure is poor and railways absent.
The attack comes after an Al Qaeda-linked alliance, the Support Group for Islam and Muslims (GSIM), announced last month that it was blockading Timbuktu, the historic crossroads city of northern Mali.
The impoverished state has been struggling with insecurity since 2012, when a revolt led by ethnic Tuaregs erupted in the troubled north.
The insurgency was fanned by militias, who three years later took their own campaign into central Mali, Niger and Burkina Faso, sending shockwaves across the Sahel.
In northern Mali, the regional rebellion was formally ended by a peace agreement signed between the rebels and the Malian government in 2015.
However, the fragile deal came under strain after the civilian government was toppled in 2020 and replaced by a junta.
Tensions in the region have revived in recent weeks after the UN peacekeeping mission in Mali, which has been told to leave by year's end, handed over two bases near Timbuktu to the armed forces.
The handover triggered clashes between the army and the militias and led to an angry showdown with the former rebels, stoking fears for the 2015 peace agreement.