DNA detective work has tracked down meat on sale in Japan from endangered fin and sei whales that scientists say should not be there.

These samples don't match records of whales declared by Japan in its now banned Antarctic "research" program, a scientific meeting has been told.

Instead, the detectives led by US scientist Scott Baker conclude there has been an illegal, unreported or unregulated hunt of sei and fin whale, against the rules of the International Whaling Commission.

"The are only two feasible options," said Matt Collis, campaigner for the International Fund for Animal Welfare.

"Either it wasn't just the fake science that was illegal in Japan's Southern Ocean whaling, or there is a pirate whaler, illegally smuggling whale meat into Japan's markets."

However, Japanese scientists have come up with a third possibility.

They suggest the whale meat could have been frozen since it was legally taken last century.

The whale meat puzzle was exposed at the commission's scientific committee meeting, which opens on Wednesday in San Diego.

The committee will give its verdict on Japan's plans for a new Antarctic hunt. The last program was ruled illegal by the International Court of Justice in a case brought by Australia.

In the lead-up to that decision, Professor Baker from Oregon State University submitted two reports on DNA analysis of dozens of whale meat products, bought in Japanese shops, and compared to a global genetic database.

The first report described finding 21 products that came from at least 11 individual southern hemisphere sei whales.

The sei, a temperate oceanic cousin of the minke up to 19 metres long, was last legally hunted in the southern hemisphere off Chile in 1979.

Professor Baker's researchers, who collected the whale meat over a 12-year period to 2009, also bought 19 products that came from 10 individual southern hemisphere fin whales.

These were purchased before the fin, the world's second-largest whale, was openly included in the Japanese Antarctic hunt from 2005.

Professor Baker declined to comment on the findings until after the meeting ended on June 4.

However, his paper concludes that the latest DNA classification work, based on the worldwide reference data set, "provides the most compelling evidence that the source of the IUU products is the southern hemisphere".

In response, Japanese scientist Hideyoshi Yoshida agreed that the sei whale products could be of southern hemisphere origin.

"The alternative hypothesis is that these products could have been stored from the end of commercial whaling in 1979," he said.

"This is 18 years before the first sei whale market product was purchased in 1997, and 28 years before the last product was purchased in 2007."

He said damage to the meat from long-term freezer storage could be prevented by vacuum packaging, or discarding outer portions at the time of sale.