Flash drought events can be characterised by the quick depletion of crop root zone soil moisture (rapid intensification) and hence can be termed as agricultural flash droughts. These events can have devastating impacts, such as increasing the risk of agricultural yield loss, heatwaves and increased wildfire risk, which further have cascading impacts on the socio‐economic conditions. The regional hotspots of flash droughts are analysed for winter, pre‐monsoon, monsoon and post‐monsoon seasons over India from 1981 to 2020. We assess the impact of the El Niño‐Southern Oscillation (ENSO) and the Indian Ocean Dipole (IOD) on the flash drought frequency (FDF: number of flash drought events). The causal connection of the FDF with the ENSO and IOD is analysed using the PCMCI (Peter and Clark's algorithm combined with the Momentary Conditional Independence) algorithm. The monsoon season (June–September) is found to be more prone to flash droughts with higher spatial/regional average values of total per pixel FDF during the 40‐year period over the Central Northeast (~54) and West Central (~41) regions. It is observed that the fraction of the total number of flash droughts during the El Niño years (38.8%) is higher as compared with that in La Niña years (25.7%). It is also found that the co‐occurrence of positive/negative IOD with the El Niño phase can alter the seasonal fraction of FDF over India, highlighting the high complexity in the ENSO–IOD interactions. The causal analysis shows that only the Southern Peninsula and West Central regions have significant direct and lagged causal links of average per pixel FDF with IOD. Whereas, similar (direct and lagged) causal connections are observed between the ENSO and IOD. This study reveals that flash droughts and their teleconnections vary greatly among the seasons and regions in India, limiting its accurate predictions and increasing the risk to agricultural communities.