Human Rights Watch, in a 105-page report compiled from 10 months of research, said it found grave circumstances of deprivation and basic violations of civil liberties in South Sudan's prisons.
Daniel Bekele, director of African programs at Human Rights Watch, said researchers uncovered severe flaws in South Sudan's justice system.
"Many of South Sudan's prisoners are incarcerated following flawed arrests and prosecutions, detained without any solid legal justification, or sentenced for behavior that quite simply should not be criminalized as to do so is a violation of basic rights and freedoms," he said in a statement.
The research was conducted in 12 of the country's 79 prisons were detainee populations were the highest. Human Rights Watch said 30 percent of the prison population hadn't been convicted of an offense, most had no legal representation and some of those incarcerated were in prison because of mental disabilities.
The research was conducted in a 10-month period before and after South Sudan became an independent country in July 2011.