In Japan, the combined effects of declining birth and marriage rates have accelerated population decline, leading to spatial porosity and fragmentation in urbanised areas: a phenomenon known as “Urban spongification”. This study analyses local population distributions in order to identify localised low-population areas embedded within densely populated urban environments, with the aim of understanding spatial porosity and fragmentation in Osaka Prefecture. A multi-scale spatial autocorrelation approach was applied to detect the spatial extent of localised low-population areas, and results were compared between 1995 and 2020. The analysis further examined how the formation and change of localised low-population areas differ across use districts (i.e., zoning categories) and according to long-term land-use transition histories. The findings reveal pronounced spatial variability within districts that cannot be captured by conventional population density metrics alone. The study demonstrates that the emergence, persistence, and transformation of localised low-population areas are closely related to use district regulations and historical land-use processes. These results provide insights into the spatial processes contributing to urban porosity and fragmentation and offer a basis for future evaluations of residential inducement areas designated under Location Optimisation Plans.