It was gathered that they were neutralised in an operation by Nigerian military fighter jets at Lake Chad on Saturday.
Kwaya and Mainoka were influential members of the ISWAP Shura (Consultation) Council.
They died after the Air Component of Operation Hadin Kai conducted air interdiction missions at Belowa, said to be one of the ISWAP/Boko Haram enclaves in the Tumbuns, and located in Abadam Local Government Area of Borno State, western coast of Lake Chad.
The military said the strikes at Belowa became necessary after intelligence revealed the convergence of some ISWAP leaders and fighters.
The terrorists were suspected to be gathering for a meeting ahead of an attack on friendly forces.
A Nigerian Air Force fighter aircraft dispatched to the location hit the ISWAP terrorists with rockets and bombs in multiple passes.
Sources revealed that the intelligence agency confirmed the killing.
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