A spokesman for the group said its claims were based on data by Niwa and Doc and "unpublished" work.
Scientists spoken to by the Otago Daily Times said the situation was more complex than the Deepwater Group's claims made out.
Massey University veterinary pathologist Wendi Roe, who studies sea lion mortality, said it was not a simple problem and while the bacteria might be having a severe impact on pups, there would be some underlying cause.
"We don't have the answer. The most important thing is to get more information and we need a big co-operative effort to find out what the problem is."
It was likely there were multiple factors involved not just one, she said.
Niwa marine scientist Dr Jim Roberts said scientists were uncertain how the group's figure of 600 deaths was calculated.
Preliminary results from a study of population dynamics suggested young sea lion survival had been highly variable with a period of low survival from 2005.
"Klebsiella infection is one of a number of contributing factors to pup mortality."
Research on overseas sea lion species showed multiple factors could drive population change and these could interact.
"For New Zealand sea lions, disease is only one of an array of potential factors affecting population size.
"Others include mortalities in commercial trawl fisheries, predation by great white sharks and changes in the marine ecosystem that can affect the abundance of the species that sea lions like to eat."
There were other indicators of changes in the biology of New Zealand sea lions, such as a low proportion of females producing pups each year and variable milk quality, he said.
Understanding the drivers of population change was a key challenge to identifying and managing threats to the sea lions.
"We are still in the early stages of collaborative research that will help develop this understanding."
University of Otago zoologist Bruce Robertson said there had only been two pupping years where more pups died due to Klebsiella, 2002 and 2003.
"The reality is that we have never had 600 pups die each year of Klebsiella in any year. Even in the two years when there was Klebsiella outbreaks, other forms of mortality were more important."
A University of Otago modeling study showed females of breeding age were the demographic group driving the population decline, not pups, he said.
"The best thing industry could do before we all grab our drenching guns or syringes of vaccine is to show some marine stewardship and offer to stop fishing around the Auckland Islands for a few years to give the sea lions a chance to rebound from their precarious position."
A spokeswoman for Conservation Minister Nick Smith's office said on Monday the minister's response to the Deepwater Group's claims was coming. It had not been released yesterday.
