Boko Haram militants have killed dozens of people and burned down homes in the north-east Nigerian town of Baga in the past two days, in a second killing spree since seizing control there at the weekend, witnesses said.

Two locals said the Islamist insurgents began shooting indiscriminately and burning buildings on Tuesday evening in raids on the civilian population that carried on into Wednesday.

“I escaped with my family in the car after seeing how Boko Haram was killing people … I saw bodies in the street. Children and women, some were crying for help,” Mohamed Bukar said after fleeing to the state capital Maiduguri.

The insurgency killed more than 10,000 people last year, according to a count by the Council on Foreign Relations in November. It is seen as the gravest threat to Nigeria, Africa’s biggest economy, and a headache for the country’s president, Goodluck Jonathan, ahead of an election on 14 February.

Soldiers fled Baga over the weekend when the Sunni jihadist group overran a nearby army base.

The district head of Baga, Abba Hassan, said on Thursday that at least 100 people were killed during an attack at the weekend when the group first took over the town on the edge of Lake Chad.

Abubakar Gulama, who escaped without his family to Monguno, 40km away, said he crossed “many dead bodies on the ground” and that “the whole town was on fire“.

Reuters TV footage showed scores of civilians waiting on sandy streets on the outskirts of Baga to catch buses out of town. Many carried the few possessions they had salvaged, such as bags of clothes and rolled up mattresses.

In the last week, about 2,000 Nigerians and 500 Chadians have fled Boko Haram attacks in Chad’s Lake region, Chadian prime minister Kalzeubet Pahimi said on Wednesday.

A source at a rights group in Maiduguri said some 10 women who snuck out of Baga a few days after the first attack had reported that their daughters aged between 10 and 20 had been kidnapped.

The militants have been waging an insurgency to establish an Islamic state for more than five years.

The number and scale of attacks rose sharply in 2014 after the government imposed emergency rule on the three worst-hit states in 2013, and the administration of President Jonathan has met growing criticism for failing to quash it.

Jonathan defended his record on tackling Boko Haram at the launch of his election campaign and blamed opposition candidate Muhammadu Buhari for Nigeria’s ill-equipped army.

Boko Haram has taken over or rendered ungovernable swaths of the north-east, especially Borno state where Baga is located. It has also launched attacks in Chad and Cameroon, while Chad has appealed for international aid to support the refugees coming across its border.