Trends in nitrogen (N) and phosphate (P) balance for several crops were calculated for the nation and by prefecture for 5-year periods from 1985 to 2005. Prefectural chemical N and P fertilizer applications for paddy rice and upland crops declined but applications for vegetable crops increased during the period like as national trends. Prefectural chemical N and P applications for tea, orchard and forage remained unchanged in line with national trends. Manure N and P applications for each crop did not follow the trends for chemical fertilizer. Although chemical fertilizer application declined, N and P crop withdrawal for paddy rice, upland crops and tea increased as a result of optimizing fertilizer timing and placement. Nitrogen and P balance for each crop indicated a surplus; P surplus was larger than N surplus, because of higher P input and lower crop P withdrawal. Chemical N fertilizer determined N surplus except for forage, which was determined by manure application. Therefore N surplus on paddy rice, upland crops, orchard and tea declined and increased on vegetables. Forage recorded an N deficiency in two 5-year periods nationally because of low manure input. Because P balance was also determined by chemical P fertilizer, the P surplus for paddy rice and upland crops declined and the P surplus for vegetables increased during the period. Total P surplus was reduced on paddy rice and upland crops. Trends for chemical fertilizer, manure and N and P balance varied widely among prefectures, especially for P. Crop withdrawal of N and P varied relatively little. Although prefectural trends did not always follow the national trend, we could conclude that the negative environmental effects of Japanese crop production have diminished recently, and an improvement in N and P balance in vegetable production can be expected.