Nigerian President Goodluck Jonathan fired his national security adviser and defence minister on Friday, his spokesman said, as fears mounted over spiralling unrest in the country's north.

Nigeria has faced a deadly insurgency from Islamist group Boko Haram, who have launched a bloody series of bomb and gun attacks.

"The NSA (national security advisor) has been dropped... The minister of defence has also been dropped," Jonathan spokesman Reuben Abati told AFP.

He said the new security adviser would be Sambo Dasuki, a retired colonel, prominent northerner and cousin to the Sultan of Sokoto, Nigeria's highest Muslim spiritual figure.

Dasuki was also implicated in a 1995 coup attempt against the government of former dictator Sani Abacha and went into exile in the United States at the time.

It was not yet clear who would replace defence minister Bello Mohammed.

Amid the Boko Haram insurgency, criticism of Jonathan greatly intensified this week after three suicide bombings at churches sparked reprisals from Christian mobs who burnt mosques and killed dozens of Muslims.

There have been growing warnings that there could be more cases of residents taking the law into their own hands if something is not done to halt the Boko Haram attacks.

Nigeria, Africa's most populous nation and largest oil producer, is divided between a mainly Muslim north and predominately Christian south.

The fired national security adviser, Owoye Azazi, is a political ally of Jonathan's, with both men from Bayelsa state in the oil-producing south.

Azazi faced suspicion in the north, particularly after comments he made in April which many took as indicating that the violence was politically linked.

The decision was announced after Jonathan met with his security team on Friday, hours after returning from a UN environmental summit in Brazil.

Jonathan's decision to leave Nigeria on Tuesday for the summit as fresh riots broke out had also drawn heavy criticism.

Several days of unrest in parts of northern Nigeria began Sunday in Kaduna state, with suicide attacks at three churches that killed at least 16 people and sparked reprisals by Christian mobs, who burned mosques and killed dozens of Muslims.

More rioting broke out in Kaduna later in the week, while on Monday and Tuesday, shootouts between security forces and suspected Islamists in the northeastern city of Damaturu left at least 40 people dead.

At least 106 people were killed in the days of violence.

The initial suicide bombings were claimed by Boko Haram, whose insurgency concentrated in the north has killed hundreds.

Criticism has mounted over the government's response to the violence, with few public indications of what strategies are being employed beyond heavy-handed military raids to stop the onslaught of attacks.

"Since these terrorist acts began, nothing the president... has done has been reassuring that the end to this spate of bombings and gun attacks is in sight," the Christian Association of Nigeria, the country's main Christian body, said this week.

"On the contrary, his utterances after each bombing and killings, even if unwittingly, seem to have cast a hallmark of weakness on his presidency and an escalation of the terrorist acts."

Shehu Sani, a prominent rights activist based in Kaduna, welcomed the firing of the two officials, but said it was not enough.

"The sacking of the two men will not in any way end the insurgency and the pervasive insecurity in the country without a comprehensive and sincere dialogue and peace process that will lead to permanent peace," he said.

Boko Haram initially said it was fighting for the creation of an Islamic state, but its demands have since repeatedly shifted and its structure has become less clear. It is believed to have a number of factions, including a main Islamist wing.

Many say deep poverty and frustration in the north have been main factors in creating the insurgency.

The United States on Thursday said it had designated the head of the main branch of Boko Haram, Abubakar Shekau, a "global terrorist" along with two others tied to both Boko Haram and Al-Qaeda's north African branch.