On a tip-off, the Nigerian Army launched the raid on a suspected hideout of Boko Haram members in Kawuri area of the state shortly before setting out on a planned attack on Konduga.
The statement added that one fabricated artillery gun, two anti- aircraft guns, an armored vehicle and assorted types of ammunitions were seized in the process.
Some hardware, weapons, food items and personal belongings were also destroyed in the raid, said the military statement, noting that one officer and two soldiers were seriously wounded.
Boko Haram, which claimed responsibility for recent deadly attacks in northern Nigeria, has seized a number of towns and villages in southern Borno and near the border with Cameroon.
The Nigerian forces have been raiding militant camps and launching air and ground attacks on suspected hideouts of the militants over the past three months.
Activities of the Boko Haram sect have recently been on the increase in Borno, which shares a border with Cameroon, Niger and Chad.
The sect seeks to enshrine the Islamic sharia law into the constitution and declares war against Western education.