A Nigerian soldier shot and killed a humanitarian worker, another soldier and wounded a UN pilot in the northeast of the country where security forces are fighting a grinding jihadist conflict, the UN and the army said.

On Thursday at a military base in the northeast, the soldier shot and killed a staff member of an NGO providing humanitarian aid in the region, said military spokesman Samson Nantip Zhakom.

The UN on Friday said the "apparently rogue soldier" had killed a female aid worker employed by French organisation Medecins du Monde in Damboa in Borno State, but did not give details on the victim's nationality.

"Same soldier also killed another soldier and injured the co-pilot of one of the UN helicopters, the military spokesman said. "Own troops on the ground immediately neutralized the errant personnel."

Neither the military nor the UN gave a reason for the shooting, but the army said it was investigating.

The Nigerian armed forces are battling the Islamic State West Africa Province and Boko Haram jihadist groups in a conflict that has killed 40,000 people since 2009 and displaced two million more.