El Nino a warming of sea-surface temperatures in the Pacific can trigger drought in Southeast Asia and Australia and floods in South America, hitting production of key foods such as rice, wheat and sugar.
The potential disruption to supply would come after many crops have already been hit by adverse weather in the Northern Hemisphere that has been in the grip of a savage winter.
The El Nino predictive model predicts the sea temperatures in the ocean area monitored for El Nino will transition from a level near standard this spring to a higher than standard level this summer, the Japan Meteorological Agency said in a monthly online bulletin about the phenomenon.
Last month, the bureau had pegged the possibility El Nino emerging or not as equal. The US weather forecaster said last week the much-feared weather pattern could strike as early as the Northern Hemisphere summer.