The impact of whaling from last century pushed many whale species almost to extinction, with some species still below their pre-whaling numbers.
The findings highlight the importance of krill populations to assist recovery of whale populations.
Scientist Dr Viv Tulloch, who led the study, said this was the first time scientists had been able to link climate change to the future abundance of krill and how this could influence whale populations in the Southern Hemisphere.
"Krill is the main food source for whales, so we linked possible changes to krill levels in our southern oceans based on high carbon emissions predictions to whale populations in these areas," Dr Tulloch said.
"We found that the impacts on whale species could differ, depending on the region and where they feed.
"Whale populations in the Pacific Ocean, particularly Blue, Southern Right and Fin whales, could have less krill to feed on than those found in the Atlantic and Indian Oceans."
CSIRO's Model of Intermediate Complexity for Ecosystem Assessment, known as MICE, was used to predict these future scenarios using data on ocean temperature, primary productivity and sea-ice.
CSIRO senior scientist and co-author of the paper Dr Éva Plagányi said the research highlighted how a changing marine environment such as increases in ocean temperatures could affect krill, and its importance for ongoing whale recovery.
"Our modelling took into consideration the slow population growth rates of whales, the connection between life history and water temperatures, and dependency on prey to highlight the need for ongoing protection of already depleted whale populations," Dr Plagányi said
View the Global Change Biology paper, Future recovery of baleen whales is imperiled by climate change.
This paper builds on a previous paper, Ecosystem modeling to quantify the impact of historical whaling on Southern Hemisphere baleen whales, published in Fish and Fisheries, to provide more information on Southern Hemisphere whale recovery.