A series of UN peace-building missions have taken the leading role in reconstructing the rule of law in East Timor, most notably through the hybridised Special Panels trials from 2000 to 2005 and ongoing hybridised participation in prosecution and judging in the years since then. While UN peace-building doctrine place great faith in transfusions of international expertise in the institutions of justice to secure their autonomy, the experience in East Timor has been one of consistent governmental interference to restrain politically sensitive prosecutions and systematic pardon of those convicted of committing crimes of political violence. Beginning with the thwarted prosecution of Indonesian generals accused of crimes against humanity before the Special Panels, and moving on to consider episodes of prosecutorial interference and systematic pardon in trials dealing with crimes committed during serious civil unrest in 2006 and attempted assassinations of the President and Prime Minister in 2008, this article examines the UN's ongoing failure to secure the autonomy of the judicial institutions it is mandated to assist. It cites a preoccupation on the part of the UN with the institutional aspects of the rule of law which has been emphasised at the expense of the more contentious cultural and behavioural aspects of the rule of law at a political level which are essential if the institutions of justice are to operate independently.