Amnesty International says hundreds of people have been detained and tortured by the South Sudanese authorities during the civil war which began in 2013.
The rights group says many of them are political detainees accused of being linked to the opposition and there have been cases of detainees being sexually assaulted.
It says there are also cases of enforced disappearances.
Amnesty says the South Sudanese government has become increasingly intolerant of any form of criticism.
A spokesman for President Salva Kiir, Ateng Wek Ateng, denied the allegations of torture and said more than 20 political detainees were recently released and no more than three were still being held.