A new ratoon rice cropping method known as the SALIBU system, which uses the lower nodes of the stubble, is gradually spreading throughout the tropical regions. In the technology package, ‘cutting twice’ has a large effect on the number of ratoons (tillers), and interestingly, the effect changed from positive to negative with changes in the management conditions used to cultivate rice. A previous study investigated conditions including fertilizing, water management, and growth stage at harvesting; however, which of these conditions has the greatest effect on the effect of ‘cutting twice’ remains unclear. We performed a pot experiment to clarify which of the level of fertilizer or the delay of harvesting time affects the number of ratoons. The results showed that with a short delay in harvesting there were almost no ratoons, a long delay in harvesting resulted in many ratoons. By contrast, the single cutting results in ratoons. This indicates the negative effect of cutting twice occur due to earlier harvesting. However, adding fertilizer results in more ratoons, and the response to delayed harvesting showed a similar tendency; in short, no reverse effect occurred due to the level of fertilizer. Harvesting earlier (at the physiological maturation stage; 25% green husk) than normal is emphasized in the SALIBU technology package. However, our results show the ‘cutting twice’ has a negative effect on the number of ratoons when harvesting early.