The South Sudanese government under President Salva Kiir is under fresh pressure to release all of the political detainees.
Human rights groups say this will guarantee certainty to a peace deal he signed recently with his nemesis Riek Machar.
Last week, Juba's Information ministry announced the government had released 21 political prisoners as part of the implementation of the new peace agreement.
Their identities were not released to the public.
But the rights groups say hundreds more continue to be held without trial and are not allowed visits from their families and lawyers.
Human Rights Watch (HRW) in their latest status report says the release of the detainees should be followed with stronger guarantees for civil liberties as well as freeing of any other people who still detained.
HRW has specifically called for the release of activists Samuel Dong Luak, Aggrey Idri and James Gatdet Dak, once a spokesman for Dr Machar, all known critics of Mr Kiir’s regime who were deported from Nairobi two years ago.
Also in detention is Dr Peter Biar Ajak, a frequent commentator on NTV AM Live show and chairman of the South Sudan Young Leaders Forum.
Dr Ajak was arrested in July at the Juba airport after authorities approached him with an arrest warrant.
"Even though his family has been allowed to visit him at the NSS headquarters in Juba, Amnesty is concerned he may be held in solitary confinement. He has been denied access to a lawyer. He is yet to be brought before a court and the reason for his arrest remains unclear," Amnesty International said in a statement.
Though a critic of Mr Kiir, rights groups say he never picked up arms and his arrest may have been linked to a youth forum he was due to hold in South Sudan.
Then there is entrepreneur and philanthropist Kerbino Wol, who was arrested in April on charges of coup attempt, planning assassination and associating with rebels.
The 36-year-old, once a child soldier but who rose to start his own security business, is among those still detained and denied contact with his family and his lawyers, even after President Kiir pardoned Dr Machar.
HRW and Amnesty International, together with several local rights groups, claim Mr Wol is among several thousands of South Sudanese that have been arrested arbitrarily and held for months, even years, without any due process during the years of civil war.
Close associates have defended Mr Kerbino, the founder and CEO of Kerbino Agok Security Services (KASS), against claims of plotting to overthrow the government and say he has no link with any political groupings normally opposed to Kiir.
They back this claim with the fact that he has not been presented in court four months.
“He has only focused his energy to giving back to the community through his philanthropic organisation, the Nile Foundation," said one associate speaking in Nairobi and who did not want to be named for fear of being targeted.
He was referring to Mr Wol's organisation that says it is a platform for youth empowerment through entrepreneurship, education and sports, trying to lure young soldiers from violence.
Moments after Kiir and Machar signed the peace deal in Khartoum earlier this month, the US, UK and Norway commonly known as the Troika, asked the leaders to "behave differently and demonstrate commitment to peace and good governance."
"We support the people of South Sudan’s aspirations to lead lives unburdened by fear, and to experience peace, pluralism, and prosperity," the countries who have mostly financed the mediation said in a joint statement.
"We remain steadfast that the best hope for sustainable peace is a process inclusive of ordinary men and women, civil society, religious leaders, ethnic minorities, and other excluded groups."
For Mr Wol, his arrest and continued detention represent an injustice to the former child soldier, rights groups say.
Born in 1982 to a humble family in Tonj state of Bahr el Ghazal region, he fled with his family to Ethiopia, aged four, from the civil war that had erupted in the then southern Sudan region of the Sudan.
He later joined the Sudan People’s Liberation Army (SPLA), then a rebel group led by Dr John Garang, at the age of twelve.
He became a member of the “Red Army,” which was like a battalion of child soldiers.
When Khartoum and Juba signed the 2005 Comprehensive Peace Agreement that provided some sort of autonomy to the south, Mr Kerbino rose through the ranks to be apart of the presidential guard detail.
But he later left the army to start KASS with a small staff of only five guards.
The company grew, offering basic security services to local businesses, NGOs and diplomatic missions and his firm has expanded with a footprint in Kenya and the DRC.