The Suai Church massacre occurred on 6 September 1999, in Suai, Cova Lima District in southwestern East Timor, two days after the results of the independence referendum were announced.

According to the International Commission of Inquiry on East Timor's report to the Secretary-General of the United Nations, several hundred persons had sought refuge in the Ave Maria church from attacks of the pro-Indonesia Laksaur militia in the city. Then the militia, with the support of the military of Indonesia, killed up to 200 people. Twenty-six bodies were identified that had been buried across the border in West Timor, but eyewitnesses claim many more were killed.

Five Indonesian officials—Lieutenant Colonel Liliek Kusardiyanto, Captain Ahmad Syamsudin, Lieutenant Sugito, police Colonel Gatot Subiaktoro, and District Head Herman Sedyono—were tried in Indonesia for these crimes but were acquitted. The UN named them and eleven other men in an indictment filed by the UN Serious Crimes Unit in Dili, accusing them of 27 counts of crimes against humanity including murder, extermination, enforced disappearance, torture, and deportation.

• List of massacres in East Timor

• ETAN (East Timor and Indonesia Action Network) page, including excerpts from the UN report and eyewitness accounts
• Human Rights Watch page discussing acquittal of the five implicated Indonesian officials
• Suai Church Massacre drawing by Suai youth & Photograph of Church
• Drawings of Massacre by Suai Youth 2000
• Short Documentary about Suai Church Massacre