A senator in Borno state said troops had abandoned the base in the town of Baga after it was attacked on Saturday. Residents of Baga, who fled by boat to neighbouring Chad, said many people had been killed and the town set ablaze.
Baga, scene of a Nigerian army massacre in 2013, was the last town in the Borno North area under government control.
It hosted the base of the Multi-National Joint Task Force (MNJTF), made up of troops from Nigeria, Chad and Niger.
Set up in 1998 to fight trans-border crime in the Lake Chad region, the force more recently took on Boko Haram.
The military, which includes Western advisers and surveillance, seems incapable of dealing with the problem
Residents who fled to Chad said they had woken to heavy gunfire as militants stormed Baga early on Saturday, attacking from all directions.
They said they had decided to flee when they saw the multi-national troops running away.
One unnamed resident of the town described what had happened. "They came through the north, the west and from the southern part of the town because the eastern part is only water. So, when we [went] towards the western part, we saw heavily armed Boko Haram men coming towards us.
"The soldiers were trying to repel the attack but that wasn't going to happen because a lot of the soldiers were without their guns and some were running into the town. When you see soldiers running away into the town - what are you to do, other than to just run away as well?"
Communications with the town were cut off and exact information about casualty numbers could not be confirmed.
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