Samson Nantip Zhakom, a spokesman for the Nigerian army, said troops at the Damboa base in Borno province took steps to "immediately neutralize" the unidentified soldier, indicating that he had been killed.
A helicopter pilot for the U.N. Humanitarian Aid Service was injured in the shooting and is in stable condition, said Zhakom of the incident which took place on Thursday.
The aid worker who was killed had worked for the group, Medecins du Monde (Doctors of the World), according to the U.N. in Nigeria.
The shooting incident shocked the humanitarian community in northeastern Nigeria where aid workers have provided life-saving assistance to millions affected by the insurgency by Islamic extremists.
The shooting prompted the U.N. air service – which transports humanitarian workers and supplies in the troubled region – to immediately suspend helicopter operations in the area.
The killing of the humanitarian worker is "deeply disturbing and sad," Matthias Schmale, a humanitarian coordinator for the U.N. in Nigeria.
"All humanitarian staff working in northeast Nigeria deserve our fullest respect for their courage and commitment to stay and deliver life-saving assistance to people in need in often difficult and dangerous circumstances. Humanitarian workers must be protected," said Schmale.
Little is known about the soldier in question or his motivation for the attack though analysts have in the past raised concerns about the mental well-being of some of the security personnel fighting the war.
"A detailed investigation into the incident and subsequent remedial actions have commenced into the highly regrettable incident," Zhakom said.