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The ongoing violence by government forces, pro-government militia groups and anti-government armed group forms the backdrop to continued harassment, arbitrary arrests, incommunicado detentions and alleged torture of human rights defenders (HRDs) by Sudanese military and security forces. Freedom of expression and freedom of association and assembly have been increasingly curtailed. In particular, NGO members, journalists and student activists have been targeted.

Human rights defenders are vulnerable to arbitrary arrest and detention by the National Intelligence and Security Services (NISS). The 2010 National Security Act grants the NISS extensive powers to arrest and detain people up to four and a half months without judicial review, and with complete impunity when the detention is arbitrary. Human rights defenders have been held incommunicado, without access to legal representation, and family visits have been refused without reasons. Detained HRDs have been often held in NISS cells that fall outside the jurisdiction of prisons laws and regulations, where they have also suffered ill-treatment and torture.

Under emergency law, human rights defenders in Blue Nile, a war zone, suffer heavy harassment. They are targeted by government and militant groups for their active work on human rights, in particular their work on IDPs. Human rights defenders and community leaders from this area have faced military trials and many have been forced to flee the country and continue their work from outside Sudan.

The crackdown on civil society that started after the decision of the International Criminal Court on 4 March 2009 to issue an arrest warrant against President Omar Al Bashir continues to this day. In addition to the initial closure of thirteen international organisations and many local NGOs, in late 2012, the Humanitarian Affairs Commission (HAC), a regulatory body governing the work of NGOs, and the Ministry of Culture ordered the closure of five local human rights and cultural organizations, including ARRY Organisation for Human Rights and Development (ARRY), the Al Khatim Adlan Centre for Enlightenment and Human Development (KACE), the Sudanese Studies Center (SSC), the Narrative and Criticism Forum (NCF) and Beit Al Finoon. HRDs who protested the closure of the organisations were arrested.

Women human rights defenders face sexual violence, prosecution and harsh punishments imposed by the government security forces. Women organisations are under intense scrutiny and struggle with laws that generally discriminate against women.