The military said they had captured an immigration officer who confessed to being an active member of Boko Haram.
His confession led to the arrest of a number of other officials.
Boko Haram has killed hundreds in northern and central Nigeria since 2009, when it launched a campaign to install an Islamic state.
The group's fighters have bombed government buildings and churches and assassinated Muslim clerics who disagreed with their views.
Their attacks have killed woman and children, Muslims and Christians.
Lt Colonel Sagir Musa said the immigration official was arrested last month while impersonating an army officer.
"He confessed to being an active member of the Boko Haram terrorist sect," said Col Musa.
"He also confessed to having been trained alongside 15 other members of the sect on weapon handling, assassination and special operations in Niger."
Col Musa said his testimony helped the military root out a number of others who had carried out attacks for Boko Haram.
Analysts have in the past said that the fight against Boko Haram was undermined because the Islamist group had managed to infiltrate the military.
Boko Haram shot to prominence in 2009 when hundreds of their members attempted to storm police stations and government buildings in Maiduguri.
The security forces quelled the rebellion and killed dozens of the sect's members, as well as its leader.
Since then, their attacks have been better organised and caused many more civilian deaths.
Nigeria is roughly divided between a largely Muslim north, and the south, where Christianity and traditional religions dominate.
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