Soil respiration contributes significantly to ecosystem respiration and is vital in the context of climate change research. In a season-long experiment we studied total soil respiration (TSR) and its partitioning into root respiration, rhizospheric respiration (RhR) and basal-soil respiration in four contrasting rice production systems: irrigated lowland (IL) (cv. Gayatri); organic nutrient managed irrigated lowland (OIL) (cv. Geetanjali); system of rice intensification (SRI) (cv. Swarna); and aerobic rice system (Aerobic) (cv. APO). We considered TSR to be the sum of root respiration, RhR and basal-soil respiration. Irrespective of the rice production system, TSR was higher at panicle initiation stage. Considering all four systems, the RhR contributed the most (59–83%) and basal-soil respiration the least (10–19%) to the TSR. Mean RhR showed the trend of Aerobic > SRI > IL > OIL across the growing seasons and indicated higher rhizosphere activities in the aerobic system. Mean root respiration showed a trend of IL > OIL > SRI > Aerobic and mean basal-soil respiration had SRI > IL > OIL > Aerobic. Soil labile carbon pools and heterotrophic populations were higher in OIL and dehydrogenase activity was higher in SRI. Microbial biomass carbon, readily mineralisable carbon, dehydrogenase activity and the heterotroph population showed positive correlations with RhR. Hence, regulation of RhR is crucial and can be achieved through rhizosphere modifications linked with labile carbon pools and soil enzymatic activities by plant physiological modification or through soil carbon stabilisation.