Three Dutch naval ships, HNLMS De Ruyter, HNLMS Java and HNLMS Kortenaer, were lost during the Battle of the Java Sea on 27 February 1942, claiming the lives of 915 sailors. Although the ships were relocated in 2002, no official action was taken until 2016 when an international diving team from the Karel Doorman Foundation discovered that the warships had disappeared. This created tension between the government of Indonesia and those countries that had lost ships in the archipelago, especially the Netherlands. A three-track cooperation agreement was set up to investigate the disappearance of the three Dutch wrecks with the aim of understanding what had happened, in order to create a better basis for cooperation in the future. The management and protection of shipwrecks from WWII is very complicated, because of the different values that stakeholders attach to them. Only with the proper understanding and consideration of the different values or significance WWII shipwrecks hold for different stakeholders can new ways of managing these complex sites be developed that have long-term effectiveness. This paper argues that different stakeholder groups from both the flag and the coastal state must work together on this issue.