On the night of September 18, 1999, a platoon of the Liberation Tigers of Tamil Eelam (also known as the LTTE or Tamil Tigers), armed with scythes and machetes, quietly crossed the rice paddies that separate the largely Tamil district of Batticaloa from the ethnically diverse district of Ampara, in eastern Sri Lanka. Moving through the paddies toward the Sinhalese farming village of Gonagala, the Tigers split into two groups, one composed solely of men, the other of both male and female cadres. As the two groups approached the houses closest to the edge of the rice fields, the villagers slept, unaware of the massacre that was about to unfold.

By morning, fifty-four people had been murdered, including twelve children. According to survivors, the group of male Tigers only killed men, while female Tigers were actively involved in the killing of women and children. In one house, twenty people had been participating in a religious ritual to mark the death of another villager three months earlier; all but one person in the house were killed during the attack, including nine members of a single family.

After the massacre, many families, particularly those living closest to the border, began leaving their homes at night, afraid of another attack.