According to Nigerian police, Zakari has been accused of attacking Nigerian customs officers in Kari in April and killing seven people, including women and children.
Zakari was arrested on Saturday during a counterinsurgency sweep of the Balmo Forest in northeastern Nigeria.
The Nigerian Police Force reported that his arrest should help them make subsequent arrests:
"Findings as well as disclosures from the suspect will assist the law enforcement agencies in tracking down some other members of the terror cell."
The police also cautioned residents in the region to "be on guard for any suspicious or strange character fleeing from Balmo Forest."
Boko Haram has claimed responsibility for abducting more than 230 girls from their school in Borno state on April 15. Parents and families of the missing have criticized the Nigerian government for failing to dedicate sufficient resources to find the missing girls.