National Human Rights Institutions (NHRIs) play a crucial role in promoting accountability for serious human rights violations, including by gathering evidence, reporting incidents, and sometimes suggesting that crimes be prosecuted. Civil society organisations (CSOs) may also encourage prosecutions through their own investigations and advocacy, as well as by contributing to NHRI activities. However, the relationship between NHRIs and human rights groups is complex. Drawing on literature concerning the effectiveness of NHRIs, this article explores the possibilities for evaluating NHRIs’ engagement with human rights CSOs in the Asia-Pacific region. These include assessing NHRI and CSO cooperation across the wide range of activities suggested by the ‘Kandy Programme of Action’. This article analyses the usefulness of such an ‘activities-based’ approach with reference to the relationship between the Commission on Human Rights in the Philippines and CSOs in securing the prosecution of serious violations. It finds that NHRIs and CSOs can productively engage across various practice areas, but these activities change over time and within different settings. Additional contextual factors, which in the Philippines have included political environments and NHRI leadership, need to be incorporated into any assessment of NHRI and CSO relationships.