The 2015 discovery of mass graves in Thailand’s Sadao district, on the border with Malaysia, led to a crack-down on people smugglers by the Thai and Malaysian authorities. Thousands of Rohingya (as well as Bangladeshi migrants) were left stranded in the Andaman Sea as smugglers abandoned their human cargo. Initially pushed back by the Thai, Malaysian and Indonesian navies, it was only after Indonesian fishermen rescued three boats that approximately 1,800 people were permitted to disembark in Indonesia’s Aceh province. The crisis in the Andaman Sea brought into sharp relief the fact that the South East Asia region lacks even the most basic regional protection (or cooperation) framework. While some states are still reticent, there have been attempts to improve government collaboration as demonstrated recently in the March 2016 Bali Declaration on People Smuggling, Trafficking in Persons, and Related Transnational Crime. This paper examines, however, how the ad hoc approach by Indonesia’s regions, in particular Aceh, to the treatment of the Rohingya who arrived in Aceh in May 2015, works against a comprehensive, national, rights-based approach to protect those seeking asylum in Indonesia. The paper explores the reasons why Aceh chose not to engage with the established practices for the treatment of asylum seekers in Indonesia and the human rights impacts this has had on those rescued. It concludes that the current situation in Aceh is not sustainable. The treatment of refugees in Aceh should be included in a broader national approach, commensurate with the treatment of refugees and asylum seekers throughout Indonesia, particularly if Indonesia is to develop a structured, rights-based approach to those seeking protection. This would then play a significant role in any future regional protection framework.