As terrified residents scattered into bushes in Baga town and surrounding villages, the gunmen unloaded motorcycles from their trucks and chased after them.
Some Residents hid under scanty bush, while some decided to wait in their homes but they were later burned alive.
By the time the weapons went quiet, local officials reported death tolls ranging from hundreds to as many as 2,000 people.
According to a report by CNN mascaraed bodies are still littered in the bushes in the area.
"It is still not safe to go and pick them up for burial," said Musa Bukar, the chairman of the local government where Baga is located.
No emergency crews will enter the villages where militants are still running amok, local authorities said.
"Baga is not accessible because it is still occupied by Boko Haram," said Sen. Maina Ma'aji Lawan of northern Borno state.
"If reports that the town was largely razed to the ground and that hundreds or even as many as 2,000 civilians were killed are true, this marks a disturbing and bloody escalation of Boko Haram's ongoing onslaught," said Daniel Eyre, Nigeria researcher for Amnesty International.
Abubakar Gamandi, a native of Baga who was away during the attack, said those trapped there are dying.
"I have been in touch with them on the phone," he said. "They told me some of them are dying from lack of food, cold and malaria on the mosquito-infested island."
Mike Omeri, a national security spokesman, said Nigerian troops are pursuing the militants.
"Security forces have responded rapidly and have deployed significant military assets and conducted airstrikes against militant targets," Omeri said. "Troops are engaged in operations to reclaim the area from the terrorists."
But Gamandi, the Baga native, said it's not true.
"From information we are receiving from residents nearby, not a single Nigerian soldier has shown up in Baga since it was seized by Boko Haram," he said. "It is all propaganda."