Inmates at 240 prisons will also have an opportunity to vote as South Africans cast their votes on Wednesday.
Minister Michael Masutha expressed disappointment at the low registered number of inmates.
He says the low number of registered inmates is a concern.
Of the 164 000 inmate population in South Africa, just 11 000 have registered to vote.
The low number is attributed to many inmates not having the required R140 needed to apply for ID book.
Also fellow prisoners discourage each other from voting as they believe this will identify other undetected crimes they may have committed.