Nigerian soldiers shot dead dozens of young men during raids in a city seen as a stronghold of a radical Islamist group, residents and a morgue worker told AFP on Friday.

The reported military operations targetted four neighbourhoods of Maiduguri, the epicentre of an insurgency by Boko Haram Islamists, blamed for killing hundreds of people in northern and central Nigeria since 2009.

Residents said the troops conducting the raids ordered males in their teens and 20s to separate from the others in the area.

In the Kalari neighbourhood they told the young men "to lie face down on the ground," then asked the rest to look away.

"All we heard were gunshots. They shot them on the spot," said the elderly religious leader, who did not want to be named.

"They did the same in three other neighbourhoods. We went to the morgue to collect the bodies and we found 48 in all."

A resident of the city's Gwange area told AFP that the alleged massacre was "like a movie scene."

The troops "picked young men from their homes and were shooting them dead before everyone and took the bodies away to the hospital. I have never seen something like this," he said, also requesting that his name be withheld.

The Sabon Lamba and Gomboru neighbourhoods were also said to have been raided.

A morgue attendant at the Maiduguri General Hospital said they "received 39 bodies yesterday which were brought in by soldiers. They all have fresh gunshot wounds."

A military source declined to comment on the allegations, saying only that if such killings had taken place they were "unjustified".

Amnesty International has charged Nigeria's security forces with committing massive rights violations, including summary executions, in the campaign to crush the Islamists. Nigeria has rejected the allegations.

In a report released Thursday, the rights group documented a series of alleged extra-judicial killings by the military and police in Maiduguri, saying such conduct had fuelled further attacks and deepened a cycle of violence.

At around midday on Friday in Maiduguri, gunmen disguised as visitors entered the home of a prominent former general, Mohammed Shuwa, killing him and one of his guests, a military statement said.

Shuwa, 79, was a key leader in Nigeria's 1967-10 Biafran civil war and served under several of the country's military leaders.

In an interview at his home in May, Shuwa showed AFP the gun he carried for protection and said he could be targetted by Boko Haram.

The military blamed Boko Haram for the killings, and the attack on Shuwa resembled those previously claimed by the group, who have often targetted notable government and military figures.

The Islamists have also attacked Christians in churches and various symbols of authority as part of an insurgency that is estimated to have left 2,800 dead since 2009, including killings by the security services.

Boko Haram has said it wants to create an Islamic state in the north, but its demands have varied widely and some analysts believe the group is now made up of various different cells.

Nigeria is Africa's most populous country with an estimated 160 million people. Most in the north are Muslim, while the south is predominately Christian.