Thoenes was shot dead on the evening of September 21, when his motorcycle taxi attempted to escape a group of armed men blocking the road, according to investigators with the U.N. civilian police force in East Timor. Eyewitnesses, including Thoenes's Timorese driver, Florindo da Conceicao Araujo, told investigators that six gunmen wearing Indonesian army uniforms shot at the motorcycle, causing it to crash. Araujo said he fled when he saw that the gunmen were preparing to fire again. He last saw Thoenes lying in the middle of the street.
Australian peacekeepers discovered Thoenes's body the next morning. Investigators determined that he was most likely murdered by members of Indonesian army Battalion 745. Thoenes died of a gunshot wound through the back, but his killers had also sliced off his left ear and made several cuts in his face, according to a coroner's report released on January 27, 2000. The mutilation is reportedly a signature of Battalion 745.
Thoenes, a seasoned journalist who had experience working in East Timor and Indonesia, was believed to be the first foreign reporter killed in East Timor since 1975, when six Australia-based reporters were killed during the Indonesian military invasion of East Timor.