The application of nanomaterials as nanofertilizers is one of the advanced solutions to overcome the excessive use of conventional fertilizers without compromising the yield. In this study, the synthesized urea-doped hydroxyapatite nanomaterials (UHN) at recommended (UHN_RD) and half-recommended (UHN_HRD) doses were compared with a recommended dose of commercial bulk urea fertilizer (BUF) and control (CNT) treatment for nutrient availability in soil and yield of rice crops. Rice was grown in 12 field columns (four treatments × three replications) by applying the fertilizer treatments at four growth stages and irrigating the columns conventionally. The crop growth parameters such as plant height, biomass, and yield were measured for all columns. The depths of ponding water and drainage were measured daily, and the water samples collected from ponding water and drainage were analyzed for ammonium (NH 4 -N), nitrate (NO 3 -N), and ortho phosphorus (PO 4 -P) concentrations. The grain yield was increased by 61, 60, and 65% in BUF, UHN_HRD, and UHN_RD, respectively, compared to the CNT treatment, which indicates that the UHN can result in a yield at par with commercial fertilizers. The concentrations of NH 4 -N, NO 3 -N, and PO 4 -P in the leachate were reduced by 69.11, 16.3, and 87%, respectively, under UHN_HRD and by 60, 10.6, and 66.3%, respectively, under UHN_RD compared to BUF. The nutrient use efficiency was the highest in UHN_HRD for nitrogen (76.5%) and phosphorus (14.27%) nutrients. The application of UHN as nitrogen and phosphorus sources revealed yield improvement and reduced leaching of nutrients. Therefore, UHN could be used both as a nitrogen and phosphorus supplement to rice crops at a reduced application rate.