Although Article 25 of South Sudan’s Transitional Constitution guarantees the freedom of association, and although the purpose of the new transitional government is to ‘restore peace, security and stability’, people who operate civil society organisations do so in extremely difficult conditions. At an operational level, CSOs face the threat of violent attack from both government forces and rebel groups, and the threat of arrest and torture from the state. In December 2015, 13 civil society members were arrested in Wau, accused of being allies of rebel groups and bringing public dishonour to the state government. It was reported that at least three of them were ill-treated or tortured. In many parts of the country, human rights defenders, even those working for the promotion of peace, are repeatedly beaten, attacked, harassed, intimidated and threatened by the National Security Services (NSS). Human rights defenders cooperating with the UN Human Rights Council have also faced intimidation and harassment. Procedurally, the formation of CSOs is governed by the NGO Act of 2003. CSOs must be approved by both the Ministry of Justice and the Relief & Rehabilitation Centre in Juba. CSOs may also be required to register with sub-national bodies. A restrictive new NGO bill approved by parliament in February 2016 empowers the government to monitor the work of civil society organisations, who must get approval to undertake any activities not specifically mentioned in their registration certificate and they face severe penalties for any breach of the new rules. The bill also limits to 20% the number of foreigners each NGO may employ, potentially hampering the work of international aid agencies operating in South Sudan.

During the recent civil war, protest was virtually impossible and the right to peaceful assembly enshrined in the Transitional Constitution was effectively suspended. People who gather in public to promote any cause run the risk of deadly attacks by security services and rebel forces alike. Although some protests do occur, violence is common and the authorities frequently use excessive force to disperse crowds. A number of civil society activists were targeted in 2015 for protesting against a lack of protection at a local market. Instead of responding to their concerns, the authorities arrested the protestors. Previously, in December 2012, more than 25 protestors in Wau were reportedly killed by the South Sudan Armed Forces. From 2015, the state also made use of the National Security Service Act that gives intelligence officers broad powers to arrest, search and detain citizens.

The right to free expression is regularly and seriously violated in South Sudan, as the state aggressively denies citizens and the media the ability to impart and receive information and opinions. Numerous newspapers and radio stations have been shut down by the authorities, who have also seized the print runs of newspapers on several occasions when inconvenient stories are published. The situation worsened after the outbreak of civil war in December 2013 as the state and rebel factions sought to quell any reporting that might shine a light on atrocities and human rights abuses being committed by them. In August 2015, President Salva Kiir threatened to kill journalists who report negatively on the country. Individual journalists faced huge risks for reporting on the conflict as many were threatened, kidnapped, tortured, suffered forced disappearances or were killed; many others were forced to live in exile. This treatment of journalists continues even with the signing of a peace accord. In March 2016, journalist and editor of El Tabeer newspaper Joseph Afandi was abducted and later found with severe burns and torture marks on his body. Two months earlier he was held by the intelligence body for criticising the ruling party for failing to protect civilians. In these circumstances, people in South Sudan struggle to gain access to fact-based and impartial reporting. Internet penetration remains low in South Sudan, with just one in seven people online as of 2014.