A decrease in the filled grain ratio (FGR) under high nitrogen (N) conditions inhibits the increase in rice yield in the tropical highlands of equatorial East Africa. We hypothesized that, under high N fertilization, the decrease in FGR is due to low temperatures during the reproductive growth stages, and that high grain yield can be achieved using cold tolerant varieties. Two cold-susceptible varieties (BW196 and Komboka) and a cold-tolerant variety (NERICA 1) were grown under 57, 114, and 171 kg N ha⁻¹ of N fertilization. Grain yield increased with a higher N fertilization rate only in NERICA 1. Shoot dry weight and total spikelet number increased in all varieties under high N conditions. Although FGR decreased with increases in N fertilization rate in all varieties, the adverse effects of high N fertilization on FGR were least observed in NERICA 1. However, temperature did not affect FGR in all N treatments, growth stages, and varieties, except for Komboka during the ripening stage under high N conditions. The findings did not support the hypothesis that high-N-induced decreases in FGR are due to low temperatures. High-N-induced decreases in FGR in Komboka were mainly attributable to the poor filling of spikelets during the ripening stage due to excess total spikelets. Factors other than filling high-N-promoted increases in total spikelet number may affect FGR in BW196 and NERICA 1 under high N conditions in Mwea.