Evaluating the reduction of virus load in water reclamation plants is important to ensuring the hygienic safety of the reclaimed water. A virus-spiking test is usually used to estimate virus reduction but is not practicable at large-scale plants. Thus, we evaluated virus reduction by ultrafiltration (UF) plus ultraviolet (UV) irradiation at a large-scale reclamation plant (1000 m/d) by quantifying indigenous F-specific RNA bacteriophages (FRNAPHs). To detect the infectious FRNAPH, we used both plaque assay and integrated culture-reverse-transcription polymerase chain reaction combined with the most probable number assay, which can detect infectious FRNAPH genotypes. For comparison, we determined reductions of indigenous FRNAPHs and spiked MS2 at a small-scale pilot plant (10 m/d) at the same time. Reductions by UF were not significantly different among the bacteriophages at pilot plants. This result suggests that indigenous bacteriophages could be used for evaluating virus reduction by UF at large-scale plants. Indigenous Genotype I (GI) FRNAPH showed the highest UV resistance, followed by GII, GIII, and GIV. The resistance of GI-FRNAPH was equivalent to that of spiked MS2. The reduction of the total infectious FRNAPHs determined by plaque assay was affected by the predominant FRNAPH genotype, presumably because of their different UV resistances. Our results reveal that indigenous GI-FRNAPH can be a good alternative indicator to spiked MS2 in view of virus reduction during water reclamation. The reclaimed water from our large-scale reclamation plant could be used for irrigation because the expected reduction (6.3 log) of indigenous GI-FRNAPH achieved the Title 22 (>5 log).