Clustered DNA damage is considered an important factor in determining the biological consequences of ionizing radiation. In this study, we successfully estimated the localization of abasic sites (APs) in DNA exposed to ionizing radiation using fluorescence resonance energy transfer (FRET) without any involvement of repair enzyme functions. A linearized plasmid (pUC19 digested by Sma I) was irradiated with: ⁶⁰Co γ rays; ⁴He² (2.0 MeV/u) particles; and the ¹²C⁵ (0.37 MeV/u) particles in the solid state. A donor or acceptor fluorescent probe with a nucleophilic O-amino group was used to label APs. The results showed that the ¹²C⁵ particle likely produced close APs within a track. The apparent distance calculated from the observed FRET efficiency (E) of around 0.10 was estimated to be approximately 17 base pairs. On the other hand, E values of ⁶⁰Co γ rays and the ⁴He² beam were less than those of the ¹²C⁵ beam, increased with increasing AP density (the average number of APs per base pair), and were slightly greater than those of randomly distributed APs. We propose that the FRET method provides a degree of localization regardless of whether an AP cluster is single-stranded or bistranded DNA damage.