Intumescence is a physiological disorder in which cell walls are disrupted. Intumescence causes leaf deformation, browning and defoliation, and commonly affects tomato plants. This is a limitation in seedling production. The causes of intumescence are not known; however, ultraviolet (UV) deficiency is considered as one of the causes of intumescence. Other possible causes include high humidity and rapid changes in the water environment. In this study, tomato seedlings were grown in a commercially-available closed seedling production system under either newly installed LEDs with a low UV light intensity or conventional fluorescent lamps sources. The relationship between the shoot/root (S/R) ratio and incidence of intumescence was evaluated. In addition, the effects of different light sources were evaluated on the xylem pressure potential in the seedlings under rapidly fluctuating water conditions. As a result, the S/R ratio of seedlings grown under LEDs, with low UV intensity, was greater than that of seedlings grown under fluorescent lamps. There was a positive correlation between the S/R ratio and the incidence of intumescence of four types of seedlings with different combinations of light sources and varieties. Xylem pressure potential decreased more in seedlings grown under LEDs, compared to seedlings grown under fluorescent lamps and dry conditions, but increased significantly when irrigated. These results suggest that reducing the occurrence of intumescence in seedling production systems can be possible by a light source that can help seedlings grow with small S/R ratios and reduce fluctuations in the water condition.