There is no genocide in northern Nigeria, the African Union Commission chairperson said on Wednesday, rejecting accusations by US President Donald Trump that "very large numbers" of Christians were being killed in Africa's most populous country.

"What's going on in northern part of Nigeria has nothing to do with the kind of atrocities we see in Sudan or in some part of eastern DRC," Mahmoud Ali Youssouf told reporters at the United Nations in New York, referring to Democratic Republic of Congo. 

"Think twice before... making such statements," he said. "The first victims of Boko Haram are Muslims, not Christians."

The extremist Islamist armed group Boko Haram has also terrorised northeast Nigeria, an insurgency that has killed tens of thousands of people over the past 15 years. Human rights experts have said most Boko Haram victims have been Muslims.

Trump earlier this month said he has asked the Defence Department to prepare for possible "fast" military action if Nigeria fails to crack down on the killing of Christians. He did not provide any specific evidence for his accusation. 

He also threatened to "stop all aid and assistance to Nigeria, and may very well go into that now disgraced country, 'guns-a-blazing,' to completely wipe out the Islamic Terrorists who are committing these horrible atrocities."

Nigeria's Foreign Ministry has said the country would keep fighting violent extremism and that it hoped Washington would remain a close ally, saying it "will continue to defend all citizens, irrespective of race, creed, or religion."

Nigeria, which has 200 ethnic groups practicing Christianity, Islam and traditional religions, has a long history of peaceful coexistence. But it has also seen flare-ups of violence among groups, often exacerbated by ethnic divisions or conflict over scarce resources.