Jabr said only five people appeared to have been maltreated in the facility and insisted that those detained were the most criminal terrorists.
However he added that he will punish those who perform torture.
Earlier, Deputy Interior Minister Major General Hussein Kamal called for a unified command over detention centers to prevent future cases of torture.
Prime Minister Ibrahim al-Ja'fari has ordered an investigation into the torture allegation but Sunni Arab politicians are demanding an international probe.
Washington says it believes the Iraqi government could carry out a credible probe and therefore there is no need for an international investigation.