The 2016 Kumamoto earthquake seriously damaged crops, agricultural lands, and agricultural facilities. The earthquake caused liquefaction across large areas in Kumamoto prefecture, including those in coastal polders used for greenhouse farming. Despite the serious damage suffered by the farms, producers in the region planned to resume tomato production that year. Because the liquefaction might have altered the soil properties, we investigated the effects of liquefaction on the chemical and physical characteristics of the soils in four greenhouses. Although the sand content increased and the water permeability slightly decreased in the soils where liquefaction occurred in some greenhouses, the changes in the soil chemical and physical properties were often minimal and were not expected to seriously reduce the plant growth. The survey on tomato growth conducted after resumption of cultivation revealed that tomato production was not influenced by the liquefaction. The results of our soil survey and the unaltered growth of the tomato plants after the resumption of agriculture indicated that liquefaction in the polders did not sufficiently affected the soils to cause reduction in tomato production in the four investigated greenhouses.