Authorities in Borno state, the heartland of Boko Haram, confirmed to Associated Press that more than 100 refugees had been killed.
Lucky Irabor, a military official, told reporters the accidental bombardment killed "some" civilians and wounded aid workers, including some Nigerians working for MSF and ICRC.
Aid groups including Doctors Without Borders and the Red Cross said members of their teams were among those injured and killed; the bombing occurred while these workers were providing food to civilians.
The carnage took place near the border with Cameroon where the Nigerian army is engaged in operations against Boko Haram.
At least 20,000 people have been killed in the conflict since it began in 2009 and more than 2.6 million others made homeless. "There were.deaths and injuries but on the actual number of casualties, we would get back to you later", Irabor told a news briefing in Maiduguri, the capital city of Borno state.
A daring attack by the Boko Haram terrorist group on the University of Maiduguri, Borno state left four persons, including a University Professor dead.
He said two soldiers were wounded, but he did not have a final toll.
Teams from the aid group Doctors Without Borders "have seen 120 wounded and 50 dead following the bombing", according to Tim Shenk, a spokesman for the organization, which is also known as Médecins Sans Frontières.
"This large-scale attack on vulnerable people who have already fled from extreme violence is shocking and unacceptable".
While saying that the military would investigate, Irabor added that "it is too early for us to determine whether it was an error or not".
It could be recalled that investigations into Boko Haram insurgency has heightened with focus on government officials giving support to the insurgents.
The jet mistook the village for a Boko Haram camp during a night raid.