Although atoll-type limestones in accretionary complexes are characterized by having high purity of calcium carbonate, some of them exhibit high phosphorus content comparatively. Such limestones are unsuitable for use in steel and carbide plants. It is important for mine development to understand the maldistribution of phosphorus in limestones. We measured phosphorus content of Carboniferous–Permian atoll-type limestones embedded in the Akiyoshi accretionary complex by using ICP-AES. Those samples were classified by age and depositional environment. We recognized that in samples from the reef-core environment phosphorus contents generally exhibit higher value in the Bashkirian and Moscovian than in the Visean, Serpukhovian, and Gzhelian. In contrast, back-reef limestones are characterized by the low content of phosphorus even in the Bashkirian and Moscovian. Phosphorus content is uncorrelated with those of iron and aluminum that are generally considered as the secondary accumulation. The high content of phosphorus in the Bashkirian and Moscovian reef-core limestones suggests the high nutrient level in seawater during the deposition of the limestones. It is probably related with rising sea-level caused by coeval super-plume activity in the Panthalassa ocean and resultant dominant upwellings.