Salt accumulation and ion imbalance caused by residual fertilizer in greenhouse cultivation have been serious problems in Japan since the 1970s, when the area of greenhouse cultivation began to increase. Because an excess of sulfate ions was considered to be the major cause of these problems, low-sulfate slow-release fertilizers (LSR) were developed. In a LSR, nitrogen is added in the urea form, and silicate is substituted for sulfate. We investigated the effects of LSR on shoot and root growth and fruit yield of tomato, compared with an ordinary slow-release fertilizer, cyclo-di-urea (CDU) containing sulfate. First, we examined the effects on early growth (for 30 days) and early root distribution in small root boxes. The reduction of shoot and root growth caused by a heavy application of LSR (1.5 g N kg^-1 dry soil) was smaller than that caused by a heavy application of CDU. Root growth was severely restricted by a heavy application of CDU but only moderately restricted by a heavy application of LSR. Second, we examined the effects of the fertilizers over a longer period of time (84 days) in larger root boxes. In this case, the fertilizer was mixed only in the surface 30 cm. Plants that received a heavy application of CDU were able to grow to some extent, even though root growth in the fertilized layer was reduced, because the same roots extended to the deeper layer, mitigating the stress. With heavy fertilizer application, plants receiving LSR yielded 159% of the fruit weight of plants that received CDU. The sugar content of the fruits decreased from 5.2% ± 0.2% with CDU to 4.8% ± 0.1% with LSR. The sap bleeding rate tended to be higher in the LSR treatment than in the CDU treatment. These results suggest that LSR imposes less osmotic or chemical stress on the root system than CDU.