The Second World War drew attention to diverse forms of military violence and the devastating impact of wartime, especially wartime occupation, on civilian populations. While the post-war trials that followed have often been remembered for establishing codified protections for civilians during conflict, they also offer a rare window into the mechanisms of military rule. Trials dealing with the so-called “denial of fair trial”, for example, shed light on the administration of military justice in occupied areas, a much-understudied facet of Japanese wartime conduct. This article analyses four post-war trials conducted by Australian and British military courts, each involving charges related to the nascent concept of “denial of fair trial” in 1946, whether explicitly as part of the charges or as context for the crimes of murder and killing. It situates this analysis within the context of the regulatory framework that informed the functioning of Japanese military justice in occupied territories in order to advance the historical understanding of this legal system, the challenges it encountered during the Asia-Pacific War and its contribution to Japan’s wartime misconduct. The article demonstrates that certain issues of fairness raised by Allied judge advocates were embedded within the regulatory framework. It also draws attention to structural weaknesses within the system which precipitated a wider streamlining of judicial procedures in the final months of war. In so doing, the article highlights the potential systemic and structural underpinnings of wartime violence towards civilians.