Most indica rice varieties show a low efficiency of transformation because of difficulties in callus formation and low-regeneration frequencies in conventional culture such as MS16 or N6 medium. Recently, some improved methods were reported for Agrobacterium-mediated transformation using mature elite indica seeds however, these procedures take a long time (5–7 months) to obtain transgenic plants and still with significantly low efficiency. In this study, we provide additional improvements in the indica rice transformation protocol introducing new selection method by tosoflavin/tflA which was based on bacterial photosensitizer and its degrading enzyme pair. We introduced direct in planta transformation using early stage of germinating rice seeds instead of usual embryogenic callus. Methods that use embryos as a starting material for inoculation with Agrobacterium are also used for comparison with the new protocol using rice seeds. Transformed cells proliferated from rice seeds obtain toxoflavin resistance, and transgenic plants are eventually regenerated from those proliferated tissues. However, we found out that tissue proliferation from indica seeds and shooting and rooting are very sensitive to minor salt nutrients in the media and need to pay attention to use indica rice specific nutrient media. The use of naturally occurring photosensitizers such as toxoflavin as selection agents appears to give rapid and unambiguous selection results owing to their unique phytotoxic mode of action. In particular, the toxoflavin/tflA selection system might be useful for generating transgenic indica rice cultivar where high false-positive backgrounds with current selection marker systems are problematic.