A special autonomy status has already been given to Papua since 2001 as Law 21/2001 agreed by the central government and the parliament. Its realization was supported by the allocation of an enormous development budget, the enlargement of the province and the extension of its financing for the next two decades. This essay analyses why separatist movements were more active throughout Papua provinces though special autonomy status and its privileges have been given since two decades ago. Field researches were conducted in provinces, municipalities and districts, as well as in cities and inlands of Papua and West Papua. Data was analysed with a qualitative methodology, for which in-depth interviews with stake-holders from different background have been made. Research findings disclose that the budget for the special autonomy has not been properly used. Some were illegally delivered to separatist movements to increase their armed struggles for independence. With a proper development planning, transparency and good supervisions, the writers recommend the extension of an extra budget for the special autonomy of the Papua provinces for the next two decades.