The Nigerian Army has killed members of Islamist radical sect Boko Haram during a raid in the northeastern city of Maiduguri.

Reports say that the raid came in retaliation to a Boko Haram attack against the military in the city, which is the group's headquarters. A spokesman for the Joint Task Force (JTF) unit confirmed that 12 members of the sect were killed in the raid.

"It was also observed that some individuals are still allowing their places of worship, business centres and residences to be used by Boko Haram against security agencies," he said. "Such acts immediately make such places to be targets and the JTF is ready to deal with the issue appropriately."

The JTF is a special squad established to combat Boko Haram.

Three soldiers were killed after a bomb blast in the area late Sunday, according to some local reports. In response to the bombing, "the soldiers just began shooting indiscriminately and set homes and vehicles on fire, forcing residents to flee," resident Abbas Miko told AFP.

Human Rights Watch (HRW) published a report saying that in the first three weeks of 2012 the armed group has killed more than 253 people.

It estimated that more than 935 people have been killed in 164 suspected attacks since Boko Haram started its violent operations in 2009.

"Boko Haram's attacks show a complete and utter disregard for human life," said Corinne Dufka, senior West Africa researcher at Human Rights Watch.

"The Nigerian authorities need to call a halt to this campaign of terror and bring to justice those responsible for planning and carrying out these crimes."

"Boko Haram is targeting and killing people in northern Nigeria based on their religion and ethnicity," Dufka said.

Maiduguri, the capital of Borno state, has seen some of the worst violence.