After serving a year in the eastern township of Batticaloa and another in Trincomalee at the Jesuit Colleges he went to Poona, India, for the study of Theology.

After returning to Sri Lanka in April 1956, he was assigned to St Joseph's College in Trincomalee as a teacher and sports coach from 1956 to 1978.

Hebert was a prominent member of the Batticaloa Peace Committee that has interceded on behalf of the many disappeared and missing people as part of the Sri Lankan civil war with both the Sri Lankan government officials and the rebel Liberation Tigers of Tamil Eelam (LTTE) group.

Most Tamils from Valachchenai fled to refugee camps in the provincial capital of Batticaloa leaving behind a group of Catholic sisters, some girls and helpers trapped in a convent.

The Bishop of Batticaloa sent Eugene Hebert on August 13 to Valachchenai to assist the trapped sisters and others as well as a security guarantee against an attack.

Instead Hebert informed the bishop that as the situation was getting better he would leave on his own via a circuitous route through an ethnically mixed town called Eravur to Batticaloa as he had urgent matters to take care at the institute where he was the director.