The medical charity said Monday’s attack in Rann, in Borno state near the border with Cameroon, also destroyed some of its facilities and would affect humanitarian operations.
Fighters from the Islamic State West Africa Province (ISWAP) faction of Boko Haram targeted a military base in the town and torched buildings as they left.
MSF’s emergency programme manager, Hugues Robert, said a small team returned to Rann on Tuesday to assess the damage, and described the situation on the ground as “chaotic”.
“The figures we got yesterday from people who have been there… were 14 people died,” he told AFP by phone from Geneva.
Three of the 14 were soldiers, he added.
Military and humanitarian sources said on Tuesday that seven people were killed, including three soldiers.
Rann, which is some 175 kilometres (110 miles) northeast of the Borno state capital, Maiduguri, has now been hit three times since March last year.
The first attack killed three aid workers and saw three others kidnapped. Two of the three were later executed. The last attack happened in early December.
The raids are part of a wider pattern of assaults on military positions in northern Borno, which the United Nations has warned is increasingly affecting civilians.
More than 27,000 people have been killed since the Islamist insurgency began in 2009 while some 1.8 million people are still homeless and in need of humanitarian assistance.
Nigeria’s government and military have repeatedly insisted Boko Haram is a spent force and over the last year has encouraged internally displaced people (IDPs) to return.
The UN last week said attacks in and around the Baga area, also in northern Borno, had forced more than 30,000 people to flee, mostly to Maiduguri, putting extra strain on resources.
Some 35,000 IDPs were in Rann at the time of the attack. MSF’s Robert said about 10,000 had fled to the border.
Another aid worker in Maiduguri, who asked not to be identified, said many of the thousands went to the town of Bodo, and would be taken to a camp in Ngala.
“Ngala, with 80,000 IDPs, is already stretched and you can imagine the situation if these thousands from Rann move in,” he added.
Robert said the effect of the attacks on the population in Rann was “worrying” and would likely hit operations.
“Access was very difficult already. The structures and warehouses of humanitarian organisations have been affected,” he added.
“People are extremely isolated. Services were already very basic. Even that emergency response is reduced.”
The UN has said some 260 aid workers have recently been forced to withdraw from northern Borno because of the fighting.
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