The Nigerian Correctional Service (NCoS) says Abba Kyari, suspended deputy commissioner of police, is still in prison custody.
Gunmen had attacked the correctional facility with explosives on Tuesday night.
It was gathered that gunfire was heard for over 30 minutes, causing panic among residents.
Briefing journalists on Wednesday, Shuaib Belgore, permanent secretary, ministry of interior, said about 600 inmates escaped, but noted that security operatives have recaptured 300 so far.
Bashir Magashi, minister of defence, also said all Boko Haram suspects in the facility escaped.
Since the news of the prison invasion broke, Nigerians have taken to social media to express concerns over Kyari’s whereabouts.
There were also reports that Kyari was not seen during the morning prayers.
Reacting, Abubakar Umar, spokesperson of the NCoS, said Kyari did not escape from the facility.
“This is also to confirm to the general public that DCP Abba Kyari and other VIPs held in the facility did not escape. They are presently in custody, hale and hearty,” Umar said in a statement.
Kyari, who was arrested by the National Drug Law Enforcement Agency (NDLEA) on February 12, was arraigned on March 7 over allegations of drug trafficking.
Upon arraignment, Kyari and four other defendants pleaded not guilty.
However, the sixth and seventh defendants pleaded guilty and have been sentenced accordingly.
Kyari was denied bail and remanded in Kuje prison on March 28.
The suspended DCP is also facing extradition proceedings over his indictment in an alleged $1.1 million fraud involving Hushpuppi, the self-confessed international fraudster.