Magashi disclosed this during a press conference at the facility in Abuja.
Unknown gunmen had attacked the prison with explosives on Tuesday night.
But Magashi said the attackers are Boko Haram insurgents and 64 of its members, who were inmates in the facility, cannot be found.
He said: “What actually happened, they came in their numbers and released some of the inmates. We are now trying to determine the kind of inmates they released.
“We are trying to see what we can do to see that all escapees within the prison accommodation are brought back to the prison yard.
“About 994 inmates, we have about 600 already inside now. Many people are being recaptured. The people who came to do this, from the records, belong to a particular group, from all indicators they are Boko haram.
“Presently we could not locate any of them. Currently, they are about 64 of them as inmates and we could not locate them.”