We investigated the decontamination procedures used on polar deep ice cores before chemical analyses such as measurements of the concentrations of iron species and dust (microparticles). We optimized cutting and melting protocols for decontamination using chemically ultraclean polyethylene bags and simulated ice samples made from ultrapure water. For dust and ion species including acetate, which represented a high level of contamination, we were able to decrease contamination to below several μg l^ for ion concentrations and below 10000 particles ml^ for the dust concentration. These concentration levels of ion species and dust are assumed to be present in the Dome Fuji ice core during interglacial periods. Decontamination of the ice core was achieved by cutting away approximately 3 mm of the outside of a sample and by melting away approximately 30% of a sample's weight. Furthermore, we also report the preparation protocols for chemical analyses of the 2nd Dome Fuji ice core, including measurements of ion and dust concentrations, pH, electric conductivity (EC), and stable isotope ratios of water (δD and δO), based on the results of the investigation of the decontamination procedures.