This article analyzes the response of local actors to the Phaeton incident of 1808 to illustrate how ambiguous distribution of military responsibility impeded effective maritime defense in Tokugawa Japan. By situating the response as a product of the evolution of military organization in Nagasaki dating to 1640, this essay offers a new picture of the harbor's security as a deliberate, long-term system instead of ad hoc responses to periodic threats. Finally, it explores how the post-Phaeton focus on material improvements to harbor defenses, instead of more precisely defining military organization, reflected tensions between custom and rule of law pervading the Tokugawa state.