South Sudan must stop arbitrary arrests and improve the "dire" conditions in its prisons, where a third of inmates are held on remand and some without having been charged, Human Rights Watch said Friday.

"Flawed processes, unlawful detentions, and dire conditions in South Sudan's prisons reflect the urgent need to improve the new nation's fledgling justice system," the New York-based group said in a report.

"A third of South Sudan's prison population of approximately 6,000 has not been convicted of any offence or in some cases even charged with one, but are detained often for long periods," the majority without legal representation in an impoverished country with no legal aid, it said.

The research was carried out over 10 months before and after South Sudan's independence from Sudan last July after decades of civil war.

A former rebel army, that fought Khartoum for decades in the bush during decades of civil war, is now tasked with building a new nation from scratch.

"The experience of those in detention in South Sudan reveals serious flaws in the emerging justice system," HRW Africa director Daniel Bekele said.

HRW visited 12 of the country's 79 institutions that were often "damaged or crumbling" with cells that were "unhygienic, severely overcrowded and lack sufficient ventilation".

"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," Bekele said.

"Such detentions are arbitrary -- and therefore illegal -- under international law and often violate South Sudan's own constitution and laws."

HRW said that inmates often did not have enough to eat or drink and frequently got ill but did not receive treatment. Of 15 deaths in two prisons last year, most were from treatable diseases.

It said that judges often handed down long sentences and the death penalty to people who did not understand the charges.

An effective judiciary in South Sudan is "a fundamental building block for establishing rule of law and accountability," the group said.