Ahmed Abukar said that Godka Jilaow prison, which held hundreds of prisoners including suspected al-Shabab fighters, would be turned into a technical school. Prisoners would be transferred elsewhere, he said.
The prison, which was run by Somalia's intelligence agency, has been closed as part of efforts to improve the country's human rights record, he said.
There were many allegations that prisoners were tortured in the underground cells, according to human rights groups. The prison was used by dictator Siad Barre to jail his critics before he was deposed in 1991.
Many suspects have been held in the prison for years without charges, while others faced military trials, according to rights activists.
Military courts in Somalia continue to try a broad range of cases, including terrorism-related offenses, in proceedings that are far short of international standards for fair trials, according to the New York-based Human Rights Watch.
At least 23 individuals were executed in 2017 following military court convictions, the majority on terrorism-related charges, the group said.
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