Carbonate concretions, lenses and bands in the Pleistocene, Palaeogene and Upper Triassic coalfields of Japan consist of various carbonate minerals with varied chemical compositions. Authigenic carbonates in freshwater sediments are siderite > calcite > ankerite > dolomite >> ferroan magnesite; in brackish water to marine sediments in the coal measures, calcite > dolomite > ankerite > siderite >> ferroan magnesite; and in the overlying marine deposits, calcite > dolomite >> siderite. Most carbonates were formed progressively during burial within a range of depths between the sediment-water interface and approximately 3 km. The mineral species and the chemical composition of the carbonates are controlled primarily by the initial sedimentary facies of the host sediments and secondarily by the diagenetic evolution of pore water during burial. Based on the regular sequence and burial depth of precipitation of authigenic carbonates in a specific sedimentary facies, three diagenetic stages of carbonates are proposed. Carbonates formed during Stage I (< 500 m) strongly reflect the initial sedimentary facies, e.g. low Ca-Mg siderite in freshwater sediments which are initially rich in iron derived from lateritic soil on the nearby landmass, and Mg calcite and dolomite in brackish-marine sediments whose pore waters abound in Ca2+ and Mg2+ originating in seawater and calcareous shells. Carbonates formed during Stage II (500–2000 m) include high Ca-Mg siderite, ankerite, Fe dolomite and Fe–Mg calcite in freshwater sediments. The assemblage of Stage II carbonates in brackish-marine sediments in the coal measures is similar to that in freshwater sediments. This suggests similar diagenetic environments owing to an effective migration and mixing of pore water due to the compaction of host sediments. Carbonates formed during Stage III (> 2000 m) are Fe calcite and extremely high Ca-Mg siderite; the latter is exclusively in marine mudstones. The supply of Ca is partly from the alteration of silicates in the sediments at elevated burial temperatures. After uplift, calcite with low Mg content precipitates from percolating groundwater and fills extensional cracks.