Climate indicators associated with El Niño, which emerged in 2015, have now returned to neutral levels, the BOM said.
El Niño sees in a warming of sea-surface temperatures in the Pacific which can lead to scorching weather across Asia and east Africa, but heavy rains and floods in South America.
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The end of El Niño was not unexpected with climate indicators cooling in recent months, but Australia's BOM is the first major meteorology agency to declare the end of El Niño.
Farmers will now be looking for the development of a La Niña weather pattern, which typically brings wetter weather across the Asian region. The chance of La Niña is at 50 per cent, the Australian weather bureau said.
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