|A Nigerian soldier on patrol in Baga last year|
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.
Boko Haram attacks towns and villages on an almost daily basis, abducting people including young boys and girls, BBC Africa analyst Mary Harper reports.
The military, which includes Western advisers and surveillance, seems incapable of dealing with the problem, she adds.
|Map of Nigeria showing the town of Baga in Borno state|
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.
Maina Maaji Lawan, senator for Borno North, told BBC World Service civilians had run "helter skelter" - "some into the forest, some into the desert".
Communications with the town were cut off and exact information about casualty numbers could not be confirmed, he said.
"We are very dispirited," the senator added.
Confirming that the military had abandoned the base, he said people's frustration knew "no bounds" over the apparent fact that the military had not fought back.
"There is definitely something wrong that makes our military abandon their posts each time there is an attack from Boko Haram," the senator said. Gee, ya think?
Goodluck Jonathon's promise to destroy Boko Haram is off to a modest start. The last government controlled town in northeast Borno state should have been an impenetrable fortress, but instead, it's so weak that the military abandon the civilians and run for their lives.
The Nigerian military, like the government, is utterly inept, corrupt, and incapable of protecting its people, or completely indifferent to their fate. They did not make one single attempt to retrieve the Chibok girls, or any of the hundreds of other women and children kidnapped by Boko Haram. It is now too late to save them, they have been integrated into the militant gang of murderers and rapists.
Boko Haram is consolidating its hold on much of Borno state and there seems to be nothing anyone can do about it. The military appears to have done more harm than good in Borno.
|Goodluck Jonathon, Abubaker Shekau - leader of Boko Haram,|
anxious family after kidnappings from Chibok school
In April 2013, at least 37 people were killed and 2,275 homes destroyed in Baga by troops hunting Boko Haram fighters who had attacked a patrol, Human Rights Watch reported.
The New York-based organisation accused soldiers of engaging "more in destruction than in protection".
Before Saturday's attack on the town, the area was already a stronghold of Boko Haram, which has been waging a bloody insurgency to create an Islamic state since 2009.
More than 2,000 people were killed in militant violence last year in the north-east.
Days before the attack on Baga, suspected Boko Haram militants kidnapped about 40 boys and young men in a raid on the remote Borno village of Malari.