The National Centre for Hydro-Meteorological Forecasting said El Niño is likely to intensify over the next three months and persist between October and December.
Although El Niño typically brings below-average rainfall, forecasters warned that short bursts of extreme rain could trigger rapid inflows into reservoirs, particularly smaller ones, increasing dam safety risks.
The ministry instructed local authorities to inspect dams and reservoirs, review operating procedures and strengthen the capacity of reservoir management agencies.
Operators of gated reservoirs were also told to test floodgate equipment, power systems and monitoring facilities, while preparing flexible operating plans for heavy and extreme rainfall to ensure dam safety and reduce downstream flooding.
Authorities were instructed to limit water storage at ageing or unfinished reservoirs that do not meet safety requirements and prepare emergency response plans under Vietnam's "four-on-the-spot" disaster response principle.
Reservoir operators were also told to maintain round-the-clock monitoring during the rainy season and regularly update hydrological and operational data to support flood management and emergency response.