A military official confirmed an Air Force fighter jet on a mission against Boko Haram extremists mistakenly attacked the camp in northeast Rann, near the border with Cameroon.
The Borno state government official is helping to coordinate the evacuation and treatment of wounded – many of which are aid workers and humanitarians.
Military commander Major General Lucky Irabor confirmed that aid workers among the wounded and at least 100 people have been killed in the incident on Tuesday.
Two soldiers were also wounded, but a final toll of injured and dead has not yet been calculated.
Maj Gen Irabor said: “Somehow, some civilians were killed. We are yet to ascertain the number of persons killed in the air strike.
“Many civilians including personnel of International Committee of the Red Cross and Medicins Sans Frontieres were wounded.”
The mission had been ordered based on geographic coordinates amid information that Boko Haram insurgents were gathering.
But Maj Gen Irabor claimed it was too early to say if a tactical error was made, but he would push for an investigation.
This is believed to be the first time Nigeria’s military has admitted to making such a mistake, Express reported.
Extremist group Boko Haram stepped up attacks in the last few weeks as the end of the rainy season has enabled its fighters to move more easily in the bush.