Two Nigerian Air Force jets bombarded fighters who had gathered for prayers in Balla village, some 40 kilometres from Damboa, on the edge of the Sambisa Forest, last Friday.
"Shekau was wounded in the bombings and is believed to be receiving treatment near the Nigerian border with Cameroon around Kolofata," a source with contacts within Boko Haram told AFP.
"His deputy, Abba Mustapha, alias Malam Abba, was killed in the attack along with another key lieutenant, Abubakar Gashua, alias Abu Aisha," he added.
"Among them is his deputy called Malam Abba. They suffered heavy casualties because the bombings targeted a large gathering of his followers attending Friday prayers."
There was no immediate comment from the Nigerian military when contacted by AFP. The authorities have previously claimed to have killed Shekau on at least three occasions.