Nigeria's army has killed 12 suspected fighters from the Boko Haram Islamists during a raid in the northeastern city of Maiduguri, the group's base, a military spokesman told AFP on Monday.

Spokesman Hassan Mohammed of the Joint Task Force said there was a shootout in the city late Sunday between soldiers and "gunmen suspected to be members of Boko Haram... in the encounter 12 members of Boko Haram were killed."

Residents said that raid came in response to a Boko Haram attack against the military in the violence-plagued city.

They accused the army of going on a rampage in one neighbourhood after the Islamist attack, forcing some residents to flee their homes.

Asked about the crackdown and reports of military misconduct, Mohammed said: "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."

"Such acts immediately make such places to be targets and the JTF is ready to deal with the issue appropriately," he said.

The JTF is special squad established to combat Boko Haram, a extremist group with unclear motives that has killed more than 200 people already this year in Africa's most populous nation.

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

Residents of the city's Budum neighbourhood said that three soldiers were killed by a bomb that went off in the area late Sunday, but the JTF denied those reports.

In response to the bomb blast, "the soldiers just began shooting indiscriminately and set homes and vehicles on fire, forcing residents to flee," resident Abbas Miko told AFP.

He said hundreds of people had left their homes.

Babagana Alkali, the son of the area's top Muslim leader, also accused the army of shooting at civilians.

Soldiers in Maiduguri have in the past been accused of reacting with indiscriminate violence following Boko Haram attacks, but the military has rejected those claims.

The security forces have faced mounting pressure to contain the Boko Haram insurgency, which has intensified in recent weeks through a wave of both large and small scale attacks.

The group killed at least 185 people in coordinated gun and bomb attacks in Nigeria's second city of Kano on January 20, its deadliest ever strike.

That assault, like much of the group's recent violence, primarily targeted the police.

Much of the violence has been concentrated in Nigeria's deeply-impoverished, mainly Muslim north. The southern part of the country is predominantly Christian.