Spokesman of the 7 Division of the Nigerian Army, Lt. Col Muhammad Dole said the troops launched an offensive on the sect camp along Rimanti Allagarno road in Damboa Local Government on Thursday.
"Nine of the sect members died while others fled with various degrees of injuries," Dole said in a statement.
He disclosed that large number of arms and ammunition were recovered with two pickup vehicles and two motorcycles during the encounter.
Military troops were intensifying patrol and surveillance
The army spokesman said military troops were intensifying patrol and surveillance in the forest around Damboa and Gwoza Local Governments "to reach remote and isolated towns and villages with a view to preventing further incessant attacks by the insurgents".
He described the insurgents as "desperate and frustrated elements", insisting that insurgents camps, hideouts, vehicles were being destroyed by the troops.
Dole urged the people to assist the military with useful information to end insurgency in the northeast state.
The military has stepped up the fight against the extremists, killing more than 100 members of the sect in Yobe and Borno states more than three week ago.
The Boko Haram sect poses the biggest security threat in the West African country. Hundreds of people have been killed since it launched the insurgency in 2009.