Whole crop rice (WCR) cultivation is expected to establish a recycling system that exchanges feed with manure from livestock farming. Since WCR cultivation focuses more on above-ground biomass rather than grain quality, farmers tend to apply excessive amount of manure. Excessive application of manure leads to water pollution such as eutrophication and groundwater pollution. Thus, assessing nutrient balances in a paddy field is important to appropriately apply manure in WCR cultivation considering environmental impacts. The objective of this study was to assess NPK balances in actual paddy fields where WCR was cultivated under different manure and chemical fertilizer applications. Field surveys were conducted on 8 fields in both 2013 and 2014 and additional two fields were surveyed only in 2014 (i.e. 10 different fields and 18 observations in total) in the Itoshima region, Fukuoka Prefecture, Japan. The surveyed fields included two application methods of manure (M) alone and chemical fertilizer (CF) alone. The Tachiaoba cultivar (Oryza sativa L.) was cultivated in all surveyed fields. NPK balances were assessed by differences between NPK input in a paddy field and NPK output from a paddy field in 2013 and 2014 (i.e., NPK input-output balances) and by differences in the amount of soil total nitrogen (TN), total phosphorus (TP), and total potassium (TK) between after harvest in 2014 and after harvest in 2013 (i.e., soil NPK balances). Residual N, P and K, which were calculated as NPK input-output balances, were markedly large in M fields: 390–1174 kg N ha-1, 100–489 kg P ha-1, and 168–968 kg K ha-1, respectively. Contrarily, residual N, P and K were small in CF fields: 40–74 kg N ha-1, 1–8 kg P ha-1, and −18 to 24 kg K ha-1, respectively. Excessive application of manure beyond crop requirement resulted in large residual N, P and K, which can cause water pollution through leaching and surface runoff. Moreover, positive trends of soil N and P balances in M fields implied that large amount of manure application accumulated N and P in the paddy fields. Applying manure to meet crop requirement on available P basis, which considers residual effects of continuous application and compensates for shortage of N using fertilizer, is a possible measure to produce yields comparable to N-based manure application with low environmental impacts.