Upon his departure from South Africa, Haugen began work for the Lawyers Committee for Human Rights, based in New York City. In the late 1980s, Haugen conducted a structural examination of the Philippine government's prosecution of human rights abuses committed by its military and police. Haugen investigated multiple murders and other violent abuses by the Philippine military and police, and participated in the exhumations of victims and the provision of protection services for witnesses. In analysis of his investigations, Haugen authored a book published by the Lawyers Committee entitled "Impunity: Human Rights Prosecutions in the Philippines".