A top US general visited Nigeria on Tuesday after recently warning that collaboration between Islamist extremist groups in the region posed risks Africa-wide as well as to Europe and the United States.

General Carter Ham, head of US Africa Command, met President Goodluck Jonathan of Nigeria, where Islamist extremist group Boko Haram has been carrying out a deadly insurgency in the country's north and centre.

Ham recently spoke of concerns over indications of collaboration between Boko Haram and an Al-Qaeda affiliate in northern Africa, which he warned has found a safehaven in northern Mali, where Islamists have taken control.

A statement from Nigeria's presidency said Jonathan discussed issues including Boko Haram and asked for US support in resolving such problems.

"President Jonathan also briefed General Ham on his visit to Mali and the efforts by ECOWAS to resolve the conflict in that country, adding that the situation could still be contained if the right steps are taken quickly," it said.

Jonathan attended an October summit in Bamako to discuss winning back northern Mali from the Islamists.

ECOWAS, a 15-nation regional bloc, says it wants to deploy 3,300 troops to reclaim northern Mali and is waiting for approval from the UN.

Meanwhile, Malian Prime Minister Cheick Modibo Diarra quit Tuesday under pressure from influential former putschists who are opposed to a military intervention.

Ham recently told an audience in Washington that he was concerned about indications of growing links between African extremist groups that could pose a threat across the continent as well as to Europe and the United States.

"We have seen clear indications of collaboration amongst the organisations," he said.

"In one instance ... we believe and have seen reports that Boko Haram is receiving financial support, probably training, probably some explosives, from Al-Qaeda in the Lands of the Islamic Maghreb, and in a relationship that goes both ways."

There has long been intense scrutiny over whether Boko Haram is forming operational ties with other extremist groups.

Diplomats have said previously that there has been evidence of Boko Haram members seeking training in northern Mali, but not of operational links.

The US has declared three Nigerian extremists "global terrorists," but has declined to label Boko Haram as a whole a terrorist group due to its nebulous nature and domestic focus, among other factors.

It is believed to include various factions with differing aims, in addition to imitators and criminal gangs that carry out violence under the guise of the group.

Nigeria is Africa's most populous nation and largest oil producer. Its 160 million population is roughly divided between a mainly Muslim north and predominantly Christian south.