The IOM office in Kupang, West Timor, provided emergency transportation to some 1,500 people who had fled violence in Ambon, the provincial capital of the troubled Moluccan Islands. They arrived in the night of 18 July on board the inter-island ferry, the KM Dobon-Solo. As the ship docked in the port of Kupang, people poured out of the ferry which was filled to more than double its capacity. Dozens of the newly arrived told IOM that they were forced to take smaller boats or swim towards the waiting ferry that was anchored off shore, out of the danger zone. The majority of the people assisted by IOM managed to flee with just the clothes on their backs.
According to those who managed to escape, thousands of civilians were left stranded in Ambon. Passengers who had boarded the ferry in Papua said they could hear shots and explosions as they waited anxiously off shore for the mainly Christian Ambonese to reach the ship.

Already coping with more than 100,000 East Timorese refugees, the governor of West Timor asked IOM to provide transportation for the displaced from Ambon. IOM buses and trucks took the newly arrived from the port of Kupang to hastily set up shelters on the grounds of the Christian University of Kupang and the Youth Christian Community Centre.

Since the conflict between Muslim and Christian communities erupted in January of 1999, hundreds of thousands have been forced to flee their homes and more than 4,000 people have lost their lives.

Press reports indicate that the roots of the conflict are not so much in religion as in a whole range of local disputes between the different communities, which were ignored or suppressed during the three-decade rule of President Suharto.