The incident began when gunmen in several trucks attacked a military base and a local market in the town of Kukawa late on Monday, briefly forcing troops out of the base.
"Our soldiers engaged the terrorists in a fierce battle following the attack," a military officer told AFP from Maiduguri, the regional capital which lies about 180 kilometres to the south.
"So far, 16 soldiers are missing but search teams are combing the general area to locate them," said the officer, speaking on condition of anonymity.
There were no immediate reports of casualties on either side but a civilian militia group confirmed that 16 soldiers were missing and also said one civilian had been killed in the crossfire.
Last month two Nigerian soldiers were killed when troops on foot patrol stepped on a mine around Kumshe.
Boko Haram has intensified its attacks on military targets in the northeastern states of Borno and Yobe in recent months.
(This story has not been edited by Business Standard staff and is auto-generated from a syndicated feed.)