As JTF reportedly searched through the sect’s suspected enclaves in the city, the group’s members allegedly resisted the onslaught.
This led to booming sounds of guns and bombs all through Tuesday night.
The fight continued on Wednesday.
Many residents of the city fled, for fear of being caught in the crossfire.
Witnesses said the gun battle focused on the West End area of the city to Custom and Shehuri area
JTF apparently moved to dislodge the sect’s members after receiving threats that soldiers and security agents would be attacked.
Residents of Lawan Bukar area in the city fled their homes for fear of being caught in the battle.
The Associated Press said the military confirmed that it had killed 16 suspected “Boko Haram terrorists” after hours of gunfire.
Witnesses, however, said civilians were hit by stray rounds.
A resident said JTF soldiers ambushed and killed 50 more suspected Boko Haram gunmen at Railway Quarters in the city.
“Some suspected Boko Haram terrorists attempted to open fire on (security) operatives but could not succeed.
“We have so far shot dead 16 of the terrorists during a shootout,” Col Ebhaleme told Reuters news agency,” said JTF spokesman Col. Victor Ebhaleme