Human rights defenders in Rwanda have been subject to harassment, intimidation, threats, arbitrary arrests, fabricated charges and unfair trials, and some have been forced into exile. Government-sponsored infiltration into independent human rights organisations is also reported. The work of human rights defenders in Rwanda is undermined by the authorities' claim that human rights defenders encourage 'genocidal ideology' and 'ethnic divisionism', playing on fears which are still prevalent following the 1994 genocide.

In Front Line report 'Front Line Rwanda: Disappearances, Arrests, Threats, Intimidation and Co-option of Human Rights Defenders 2001 – 2004' it was reported that the government “equated human rights monitoring, civic education, rights-based development, and any criticism of Government policy with genocidal ideology”. In 2004, a Parliamentary Commission targeted several non-governmental organisations (NGOs) as well as independent press, churches, and schools. Since then, self-censorship within human rights organisations was widespread to avoid confrontation with the authorities.

A new law criminalising genocide ideology was introduced in 2008. As noted by the UN Special Rapporteur on human rights defenders, the vague and ambiguous interpretation of the new law “would be likely to limit any opposition even moderate to government, and restrict the full enjoyment of the right of freedom of expression and opinion”. By accusing them of inciting ethnic hatred, the authorities have closed down several newspapers. Journalists, especially those work for non-state media are particularly targeted and faced harassment, arrest, and death threats. The authorities have burst into meetings rooms organised by associations working on indigenous rights, claiming the organisation was illegal and likely to incite ethnic divisionism.

NGOs are required to apply for registration with the Ministry of Local Government, Good Governance, Community Development and Social Affairs (MINALOC), and their activities and publications are placed under close scrutiny.