However, it became clear that transmigration was not the answer to Indonesia's population and economic problems. Poorly planned and executed, it often added to the problems. Even at its peak, the movement of people out of Java was never going to keep up with population growth. Others argued that the government's predominant concern was to increase its control across the archipelago through a process of "Javanisation" or "internal colonialisation." Environmental and human rights groups also became increasingly concerned at the widescale destruction of Indonesia's hardwood rainforests and the impact the policy was having on Indonesia's indigenous peoples as land they traditionally felt was theirs was taken for new transmigration sites.

Tensions between transmigrants and the local populations grew. In some areas these boiled over with murderous consequences. The conflict between the Dayaks and Madurese migrants on the island of Kalimantan is one example. In two particularly gruesome outbreaks of violence, in late 1996/early 1997 and early last year, hundreds of people were killed, including young children, many of them hacked to pieces and decapitated. Hundreds of thousands of Madurese fled their homes. Many are still living in cramped conditions in temporary camps.

Following years of economic and political turmoil across the archipelago, the situation remains explosive across much of the country. While transmigration has not been the sole cause of the violence, it has undoubtedly aggravated tensions and provided another fault line across this fragmented country. Four years after the official transmigration policy was quietly dropped by the post-Suharto government, many of its negative consequences are still being felt today and some critics argue that it is continuing under another guise. With little sign that the new democratically elected government is willing to tackle the problems created and exacerbated by transmigration, including land disputes, deforestation and massive environmental damage, and social tensions, the outlook for peace across the Indonesian archipelago seems remote.