A group of 5,000 people, most of them women and children, reached the Borno state capital yesterday after escaping the Islamists' weekend takeover of the nearby town of Monguno, officials said.
"We trekked throughout Sunday through the bushes and did not relent, even at night," said Karimu Usman, a Monguno community leader, who told reporters he led a group of 300 others on the overnight march.
Boko Haram has taken over much of northeast Nigeria and the insurgents seem capable of attacking large population centres at will.
Election officials have admitted that it will be impossible to organise polling across much of the northeast for the country's February 14 vote.
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The United Nations has said there are more than one million internally displaced people (IDPs) in the region, and hundreds of thousands of them have sought sanctuary in Maiduguri, swelling a population estimated last year at over two million.
There were 7,000 cases of cholera recorded in the city between September and December, half of them in IDP camps, and sanitation remained dire, according to MSF.
Gaal said keeping track of those displaced has been a challenge because of the relentless attacks, which has forced people to run from town to town in search of refuge.