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Indian Ocean (IO) sea surface temperature (SST) displays a warming tendency in the past 60 years, whereas the net heat flux shows a decreasing tendency. This letter examines the trends in the net heat flux into IO and its relation with the IO warming using different flux data sets derived from satellites, ship observations, and Numerical Weather Prediction reanalysis. Even though there are uncertainties in the mean flux fields, all data sets show decreasing tendency in net heat flux over equatorial IO. There is a significant increase in latent heat flux (LHF) and sensible heat flux which contributes to the decreasing tendency in the net heat flux in all the products. Linear decomposition of LHF reveals that the contribution to this increasing tendency by increasing SST is partly compensated by an increase in the surface humidity (which inhibits latent heat loss). The negative trends in net heat flux are an associated response of increasing SST, which suggests that changing oceanic processes are mainly responsible for IO warming trends and radiative imbalance plays a secondary role.