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A multi-layer ionization chamber (MLIC) which consists of a stack of parallel plate-type ionization chambers in which the parallel configuration is in the depth direction was developed at the National Institute of Radiological Science (NIRS) and has been used as a field dosimeter for MU calibration since 2002. Although the MLIC can measure depth dose distributions at one time, a correction is needed to obtain an accurate dose at the center of the spread-out Bragg peak (SOBP) in a water phantom. We attributed the observed difference between the correct dose at the center of the SOBP and the measured dose to the lack of water equivalence of the MLIC. In order to overcome this problem, a new MLIC was developed. It consists of polymethyl-methacrylate (PMMA) plates and graphite electrodes instead of flame retardant type 4 (FR4) and copper electrodes. The calibration coefficients of the MLICs were obtained by 160 MeV proton beam irradiation. For carbon-ion beams, the PMMA type MLIC has the capability to measure depth dose distributions in the water phantom with less than 2% error, including the fragment tail region.