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.
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