In Japan, rice seed are immersed in pesticide solutions to prevent seedborne diseases that attack greenhouse seedlings. However, disposal of large quantities of waste pesticide solutions after treatment is costly. As an alternative treatment, bacteriophages (phages) that are highly specific to the target bacteria are considered as potential biocontrol agents. Here, we isolated three phage strains that lyse Burkholderia glumae and B. plantarii, the causative pathogens of seedling rot and seedling blight, respectively. Two phages could lyse both bacteria and clearly suppress these diseases. One of these phages (BGPP-Ar) suppressed these diseases more effectively than existing pesticides: the ratio of seedlings exhibiting disease to the total number of seedlings examined after treatment with BGPP-Ar 1.0 × 108 plaque-forming units (PFU)/ml was 0.0 for seedling rot and 2.0 for seedling blight; after treatment with ipconazole/copper (II) hydroxide, the ratios were 14.3 and 15.0, respectively. BGPP-Ar was highly effective in suppressing seedling rot of rice, even at the low concentration of 1.0 × 105 PFU/ml. The best phage treatment effect for sterilizing seed is achieved indoors to avoid phage inactivation by UV irradiation. Treatment effect was demonstrated on seed infected with pathogens. Therefore, we consider that phage treatment was effective in this study.