The attack comes about three weeks after the Borno State Government sanctioned the return of internally displaced persons (IDPs) to the badly destroyed community which was reclaimed from the Boko Haram.
IOM said the relocation followed the reopening of the Maiduguri-Bama-Banki road on March 24 by the Nigerian military after four years of its closure due to Boko Haram activities.
The army says troops deployed in a Forward Operational Base in Benisheikh carried out the operation on Sunday at about 9.30 am, following a tip off.
A statement signed by Colonel Onyema Nwachukwu, the Deputy Director Public Relations of the Theatre Command Operation Lafiya Dole, explained that two of the men were Boko Haram commanders while the third man was a Boko Haram medic, who provided medical care to wounded insurgents.
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"Armed with the information, troops immediately mobilized to the area where they conducted a cordon and search operation".
Some Boko Haram fighters had engaged troops in a gunfight during the operation, he added.
He said that the troops acting on intelligence discovered the camp used for providing instructional training of insurgents' foot soldiers. One terrorist was killed during the encounter while other members of the group fl ed following a superior fi re power from the troops, according to army spokesperson, Brig.