A prison guide was killed in the attack in Koton Karfe, about 250 kilometers (155 miles) south of the capital, Abuja, late Wednesday, spokesman Ajayi Okansami said.
"There were people shooting and running towards the prison yard and then there was a small bomb and more shooting. Everyone ran away. We all ran away," said Ali Omale, a man who was close to the prison at the time.
The number and identities of the missing inmates are not yet clear.
But people living close to the prison fear that members of Boko Haram, a militant Islamist group frequently blamed for sectarian violence in Nigeria -- including attacks on police stations and churches -- may be among them.
Their concerns follow the recent capture of a man named as the Boko Haram spokesman Abu Qa Qa, who is from the area, and other arrests of Boko Haram suspects since December in Kaduna and Maiduguri.
Okansami declined to confirm to CNN whether members of Boko Haram were being held in the prison, saying it was a security matter that was not for public discussion.
State police commissioner Marvel Akpoyibo confirmed the prison raid had taken place but gave no further details.
Qa Qa was captured after a months-long surveillance operation, Nigerian police said earlier this month. His arrest was seen as a boost to security forces as they seek to prevent further Boko Haram attacks.
Boko Haram was formed in 2002 by Islamic preacher Mohammad Yusuf as an outgrowth of ethnic tensions in the country in the 1990s. Nigeria's population is split between mostly Muslims living in the north and predominantly Christians in the south.
Yusuf advocated the institution of Sharia law throughout the northern states and opposed democracy.
The group operated openly from northeastern Nigeria and staged small-scale attacks against government targets.
In 2009, Nigerian police forces moved to crack down on Boko Haram. Harsh police tactics led to an armed uprising and the arrest of Yusuf, who later died in police custody.
His death spurred the group to begin its attacks on police stations. Ensuing clashes between group members and the police killed hundreds.
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