The number of central Pacific El Ninos almost tripled from about 3.5 every 30 years to nine in the past three decades. The number of those forming in the thousands of kilometres to the east remained stable at about two.
The corals also revealed three of those forming in the east - 1982-83, 1997-1998 and 2015-16 -were the strongest events over the past 300 years.
"Now we have 400 years of records, and [those three] are still standing out," Dr Freund said.
During El Ninos, easterly trade winds stall or reverse, typically leading to drought in the western Pacific, such as eastern Australia and Indonesia, while producing heavy rains along the west coasts of the Americas.
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Since they also reduce the rate of ocean uptake of heat from the atmosphere, global surface temperatures also spike during such years, making El Ninos the biggest near-term influence of weather patterns.
Having more central Pacific El Ninos is not good news for Australian farmers since they tend to have the biggest influence on lower rainfall during the critical winter and spring seasons, according to the Global Precipitation Climatology Project.
Ben Henley, a researcher at the Centre of Excellence for Climate Extremes and also a co-author of the paper and a supervisor of Dr Freund's PhD, said the coral-based research offered "a very important advance".
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"Before now, we had very little idea about how these El Nino types had varied in the past," he said. "This paper gives us a unique look at that past."
While the researchers had not sought to identify a human-led climate change signal, the shift in El Ninos was "highly unusual in a multi-century context", he said.
"Some other studies have suggested strongly this could occur in the future with climate change," Dr Henley said.
Cai Wenju, a senior CSIRO researcher, said the central and eastern El Ninos have "vastly different impact" and "studies such as this one are very useful".
"Over the past 30 years, the Atlantic warming has played an important role in modulating the Pacific El Nino, leading to more central Pacific El Nino events," he said. "This can be a factor, but other studies have shown that under greenhouse warming, central and eastern Pacific events will both increase in frequency."
"Whether what we have seen in the past 30 years has already had a greenhouse warming signal needs further study," he said.
Current conditions in the Pacific favour El Nino thresholds being crossed as soon as this month, Australia's Bureau of Meteorology said last week. Any event is likely to be short-lived.
Peter Hannam writes on environment issues for The Sydney Morning Herald and The Age.