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

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.

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 when the group first took over the town on the edge of Lake Chad.

Abubakar Gulama, who escaped without his family to Monguno, 40 km (25 miles) away, said he crossed "many dead bodies on the ground" and that "the whole town was on fire."

In the last week, around 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 age 10 to 20 had been kidnapped.

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