The visit by Mustafa al-Kulaib, justice minister in the Tripoli-based government, comes after Human Rights Watch called for a probe into reported abuse of prisoners at Al-Hadba prison.
HRW made the request last week after an undated video posted on an Arab news website earlier this month showed prison guards and officials beating up prisoners including Saadi Kadhafi.
"The situation does not really reflect what people are saying," Kulaib said after touring Al-Hadba and speaking to detainees.
Kulaib said he condemns ill-treatment of detainees, but added that if such cases exist they are only "isolated incidents", promising to investigate any abuse.
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"We will work firmly against those who commit such acts in the future and will investigate all these isolated incidents."