IIn the late 1990s as the conflict in Aceh became more intense, many Acehnese fled to nearby Malaysia for security reasons. With the imposition of martial in Aceh on 19 May 2003, the numbers of Acehnese fleeing to Malaysia increased dramatically. Fearing deportation by the Malaysian authorities, many reported to The United Nations High Commission for Refugees (UNHCR) office in Kuala Lumpur. As the numbers registering increased, the UNHCR struggled to register the increasing numbers of applicants for temporary protection visas.

The problem came from the fact that the Malaysian authorities do not recognize the status of ‘refugee’ and arrested, detained and forcibly repatriating those who did not go willingly. But when the Malaysian authorities began to make mass arrests, the issue drew widespread international attention. The Malaysian government was in a very difficult position: on the one hand the Indonesian government insisted that these detainees were returned to Indonesia, while a concerned international community pleaded for them to be allowed to remain in Malaysia, at least until the situation in Aceh improved.

Since the signing of the peace agreement post tsunami, Acehnese have stopped fleeing the province to seek refugee status. There are still significant numbers of Acehnese in Malaysia, but they are there largely for economic reasons.