Scores of soldiers and civilians killed, with around 300 still unaccounted for, as insurgents storm village of Baga

Thousands of people from remote towns in north-eastern Nigeria have begun streaming into the capital of Borno state to seek refuge after Boko Haram seized an army camp in the border village of Baga, the second time the militants have overrun a military base in a week.

Fleeing residents said the village on the shores of Lake Chad – where a previous massacre left up to 185 dead – was a smouldering wreck after several hours of fierce fighting was feared to have resulted in many fatalities.

News of the attack on Saturday only began to trickle out after survivors reached the state’s capital, Maiduguri, as well as neighbouring Cameroon and Chad.

“They came, many hundreds of them, with guns, trucks and grenades,” said a Baga resident who gave only his first name, Amosun. “They burned all the houses they could reach and set the military base on fire.”

Fisherman Kumsuri Gaborou said up to 300 residents were unaccounted for, although some may have simply been lost in the chaos. Telephone lines are notoriously patchy along the porous border region, which connects Nigeria with Chad and Cameroon. Ordinary citizens and the militants move freely between all three countries.

Dozens of residents drowned while trying to flee to safety across Lake Chad, Gaborou added.

“We don’t know exactly how many lives are lost, but it was many. Some ran away into the bush and others drowned. The canoes were completely overloaded and turned upside down. I saw at least three boats of women and children all dead that way,” Gaborou said by phone from Chad, where he had fled.

Baga is notionally the headquarters of a multinational task force comprising troops from Niger, Chad, Nigeria and Cameroon, although only Nigerian troops are based there.

A Nigerian security source said troops had held back the militants for several hours until they ran out of ammunition. Some threw away their guns and fled after repeated requests for reinforcements went unheeded, he added.

A military spokesperson said the troops had fought “valiantly” but did not comment on whether reinforcements had arrived.

Dozens of other people have been killed or abducted in at least five separate attacks in Borno and Yobe states in recent days. Some residents said soldiers – who have long complained of being hampered by corrupt senior officials who funnel away money meant for arms and equipment – had deserted their posts in other villages that dot the sandy roads lined with burnt-out relics of the sect’s bloody campaign.

“You can see the Boko Haram moving around all the town in their motorcycles and trucks. They are openly moving around in large numbers,” said Yusufu Dama, who said he walked for two days to safety from Marte, a town near Baga. “Even the army are packing their families away, because they can be attacked at any time.”

An official in Maiduguri said the city was braced to receive hundreds of refugees over the next few days, many of whom would need medical treatment. “Even pregnant women and small children have trekked to us, but we’re still trying to ascertain what’s happening in those areas,” said the official, who spoke on condition of anonymity.

Up to 185 people were killed in Baga last year, making the village an early portent of Boko Haram’s new tactics of striking remote settlements before melting into the vast semi-desert surroundings.

Since being squeezed out of their urban strongholds by a renewed military push, the militants’ attacks have also spilled over into neighbouring Cameroon’s far north.

Last week the militants also briefly occupied an army camp in Cameroon’s Achigachia, prompting authorities there to launch their first-ever air strikes against the sect.

At least 15 people were gunned down in a bus shortly after New Year, while a wave of recent attacks has forced many living along the border to abandon their farms, raising the spectre of food shortages.

Attacks have also continued in Nigeria, underlining security challenges ahead of elections next month.

Last month at least 100 women and children were reportedly kidnapped and 35 people killed in Gumsuri, some 30 miles (48km) from Chibok, where 276 schoolgirls were abducted in April 2014.

Politicians have traded accusations that their rivals may provide financial or political cover for Boko Haram members in a bid to gain political leverage in an increasingly tense election runup.

More than 10,000 people were killed last year as a result of Boko Haram’s quest to carve out an Islamic caliphate in religiously-mixed Nigeria. An estimated 1.6 million people have been driven from their homes during the five-year insurgency.