The experiment was laid out in split plot design under two types of rice ecosystems i.e., puddled and aerobic with five treatments viz., Control i.e., without N fertilizer; Nitrogen in the form of prilled urea (PU); Neem coated urea (NCCU); Karanj coated urea (KCU); Vitex negundo leaf extract coated urea (VCU) at College Farm, College of Agriculture, PJTSAU, Rajendranagar, Hyderabad, Telangana state, India during karif 2013. The results revealed that significantly more uptake of N, P and K were observed in puddled rice than aerobic rice. Increased N, P and K uptake was also found with natural nitrification inhibitors (NNI) application than PU under both methods of rice cultivation. Application of NNI significantly improved the grain yield over PU applied plots under both puddled and aerobic rice cultivation methods. In aerobic rice all the NNI recorded 8.5 to 16% increase in agronomic efficiency over PU (11.9%). The highest agronomic use efficiency (AUE) was observed in KCU followed by VCU and NCCU. Similar results were obtained with puddled rice also with an increase of 8.5 to 16% in AUE over PU (11.9%). Averaged across treatments the puddled rice recorded 18% higher AUE than aerobic rice. The AUE was almost doubled with application of nitrogen inhibitors over PU plots in both methods of rice cultivation. Apparent N recovery efficiency (ANRE) of rice showed that values ranged from 19.9 to 63.5% under methods of rice cultivation with application of different NNI. Among the NNI, KCU recorded highest nitrogen use efficiency (NUE) and this was followed by VCU and NCCU. Cultivation of puddled rice with combination of nitrification inhibitors increases NUE than aerobic rice cultivation.