27-year-old Yuni Yesra Patatang was found dead in Ilaga in Papua province on Monday evening with two gunshot wounds.
The teacher was responsible for youth ministry and was a professor of religion, teaching children up to ten years old.
No one has claimed responsibility of the killing yet, however a number of armed separatist groups, unhappy with the government, operate in the area.
The Commission for Youth Ministry of the Indonesian Bishops Conference revealed that he had been killed and his body was found around 6:30pm on Monday evening.
Indonesia is a majority Muslim country, however in October 2017 the nation's Catholic youth will celebrate the National Day with young people from 37 diocese coming together for prayer.
