The Islamic State group affiliate announced on October 17 last year it had "stormed a joint position of the armies of Nigeria and Niger" in Gashagar, Borno state, killing 20 soldiers.
Local community leaders in the border area confirmed the attack at the time, saying the soldiers were caught unawares and suffered "huge casualties", without specifying how many.
Yesterday, Nigerian Army Major General Leo Irabor said the missing troops were found by soldiers and vigilantes on January 5 after clearing villages between Damasak and Gashagar.
"Subsequently, the troops recovered corpses of one officer and 15 soldiers earlier declared missing in action during their dislodgment from Gashagar on October 16, 2016."
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The bodies were discovered in a river and had since been buried with full honours, he told a news conference in Maiduguri, the biggest city in the region.
Confirmation of military casualties has been rare throughout the conflict in the remote region, as have claims and counter-claims from both sides.
But Nigeria's military has begun regular briefings to give updates on the counter-insurgency, particularly as it has gained the upper hand in the fighting.
Irabor yesterday described Boko Haram as "in disarray and... Desperate", yet attacks continue, underlining the threat from the group.
Last weekend, at least five soldiers were killed at a military base in Buni Yadi, Yobe state, while five suicide bombers killed themselves and three others in Maiduguri.