Rice yield and protein content have been shown to be highly variable across paddy fields. In order to characterize this spatial variability of rice within a field, two-year experiments were conducted in 2002 and 2003 in a large-scale rice field of $6,600m^2$ In year 2004, an experiment was conducted to know if variable rate treatment (VRT) of N fertilizer, that was prescribed for site-specific management at panicle initiation stage, could reduce spatial variation in yield and protein content of rice while increasing yield compared to conventional uniform N topdressing (UN, 33kg N/ha at PIS) method. VRT nitrogen prescription for each grid was calculated based on the nitrogen (N) uptake (from panicle initiation to harvest) required for target rice protein content of $6.8\%$, natural soil N supply, and recovery of top-dressed N fertilizer. The required N uptake for target rice protein content was calculated from the equations to predict rice yield and protein content from plant growth parameters at panicle initiation stage (PIS) and N uptake from PIS to harvest. This model· equations were developed from the data obtained from the previous two-year experiments. The plant growth parameters for the calculation of the required N were predicted non-destructively by canopy reflectance measurement. Soil N supply for each grid was obtained from the experiment of year 2003, and N recovery was assumed to be $60\%$ according to the previous reports. The prescribed VRT N ranged from 0 to 110kg N/ha with an average of 57kg/ha that was higher than 33 kg/ha of UN. The results showed that VRT application successfully worked not only to reduce spatial variability of rice yield and protein content but also to increase rough rice yield by 960kg/ha. The coefficient of variation (CV) for rice yield and protein content was reduced significantly to $8.1\%$ and $7.1\%$ in VRT from $14.6\%$ and $13.0\%$ in UN, respectively. And also the average protein content of milled rice in VRT showed very similar value of target protein content of $6.8\%$. In conclusion the procedure used in this paper was believed to be reliable and promising method for reducing within-field spatial variability of rice yield and protein content. However, inexpensive, reliable, and fast estimation methods of natural N supply and plant growth and nutrition status should be prepared before this method could be practically used for site-specific crop management in large-scale rice field.