Black-faced Spoonbill Platalea minor is a globally endangered migratory species restricted to East Asia, with a population of only 2,041 birds recorded in 2009. A total of 215 Black-faced Spoonbills has been counted wintering in Japan, and the Yatsushiro Sea, in western Kyushu is one of their main wintering sites (outside Taiwan, where the bulk of the population winters). Construction of a new bridge for the expansion of the Shinkansen (bullet train) network into Kyushu, was planned very close to an important spoonbill loafing site in the Yatsushiro Sea. Changes in the wintering situation were examined during the construction of the Shinkansen bridge (2004–2009) in the Yatsushiro Sea. Moreover, conservation approaches, including the expansion of loafing sites and the use of decoy models, were also evaluated, by conducting habitat expansion and experiments both before and during the construction phase. Initially, the number of Black-faced Spoonbills at the loafing site increased as a consequence of these conservation efforts, but this increase was only temporary and numbers gradually decreased thereafter. Eventually, the birds changed their loafing site to a neighboring river, once construction of the bridge had begun. Fortunately, their numbers in the Yatsushiro Sea have been increasing since changes to the habitat have taken place. Our observations suggest that conserving and maintaining both remaining and potential habitats are very important for the conservation of this endangered species.