Lead author Richard Zeebe of the University of Hawaii said geological records were vague and "it's not well known if/how much carbon was released" in that cataclysm.
Current carbon emissions, mainly from burning fossil fuels, are about 10 billion tonnes a year, against 1.1 billion a year spread over 4000 years at the onset of the fast warming 56 million years ago, the study found.
The scientists examined the chemical makeup of fossils of tiny marine organisms in the seabed off New Jersey in the United States to gauge that ancient warming, known as the Paleoeocene-Eocene Thermal Maximum (PETM).
United Nations studies project that temperatures could rise by up to 4.8C this century, causing floods, droughts and more powerful storms, if emissions rise unchecked.
Carbon dioxide forms a weak acid in seawater, threatening the ability of creatures such as lobsters or oysters to build protective shells.
"Our results suggest that future ocean acidification and possible effects on marine calcifying organisms will be more severe than during the PETM," Zeebe said.
"Future ecosystem disruptions are likely to exceed the relatively limited extinctions observed at the PETM," he said.
During the PETM, fish and other creatures may have had more time to adapt to warming waters through evolution.
Peter Stassen, of the University of Leuven who was not involved in the study, said the study was a step to unravel what happened in the PETM.
The PETM "is a crucial part of our understanding of how the climate system can react to carbon dioxide increases", he told Reuters. AAP