Yobe is one of three states placed under emergency rule during a three-week-old military offensive aimed at crushing Boko Haram, which has waged a deadly insurgency since 2009.
"A total of 49 suspected Boko Haram terrorists were apprehended in various locations in Yobe state," a defence ministry statement said.
"All the camps of the terrorists in the area had been dislodged as some of the insurgents fled towards Niger," it added.
Nigeria has claimed major successes in the offensive launched May 15, but the details have been impossible to verify with mobile phone networks cut across the northeast and access to conflict zones restricted.
The military has said some 200 insurgents have been arrested and dozens killed.
However in a video obtained by AFP last week, Boko Haram leader Abubakar Shekau claimed the military assault was failing and soldiers were retreating.
The United States on Monday posted a $7 million (5.3 million euros) bounty on Shekau after declaring him a global terrorist last year.
The Boko Haram conflict is estimated to have cost 3,600 lives, including killings by the security forces.
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