The state government official, who was helping to coordinate the evacuation of wounded from the remote area by helicopters, spoke to The Associated Press on condition of anonymity because he was not authorized to speak to reporters.
Military commander Maj. Gen. Lucky Irabor confirmed the accidental bombardment in northeast Rann, near the border with Cameroon, saying "some" civilians were killed.
It was believed to be the first time Nigeria's military has admitted to making such a mistake.
The International Committee for the Red Cross said six staff members and volunteers with the Nigerian Red Cross were among the dead and 13 were wounded.
"They were part of a team that had brought in desperately needed food for over 25,000 displaced persons," spokesman Jason Straziuso said in a statement from Nairobi, Kenya.Two soldiers were also wounded as well as Nigerians working for Doctors Without Borders, Irabor said, without giving a precise figure.
Doctors Without Borders said its team based in Rann had counted 50 bodies and treated 120 wounded. A statement from spokesman Etienne l'Hermitte in Geneva urged authorities to facilitate cross-border land and air evacuations.
"Our medical and surgical teams in Cameroon and Chad are ready to treat wounded patients. We are in close contact with our teams, who are in shock following the event," the statement said.Irabor said he ordered the mission based on information that Boko Haram insurgents were gathering in the area, along with geographic coordinates. It was too early to say if a tactical error was made, he said.
The general, who is the theater commander for counterinsurgency operations in northeast Nigeria, said the air force would not deliberately target civilians but there will be an investigation.