Saying the estimates were now probably "appreciably lower", the scientific committee said it could not provide any reliable estimates of current minke abundance in the region.
The International Whaling Commission (IWC) says there are fewer minke whales in the southern oceans than it had thought.
The IWC scientific committee said the true number was probably "appreciably lower" than the 760,000 estimate accepted till now.
It said it could not rule out the possibility that the Antarctic minke population had suffered a decline, which could be continuing.
And it said whaling by the former Soviet fleet in the southern Pacific had been far more destructive than the whalers had admitted at the time.
Minkes are the smallest of the great whales, reaching about 10 metres in maturity. They are also the most abundant.
Numbers unknown
The commission's scientists say the estimate of 760,000 Southern Hemisphere minkes was based on surveys conducted in the 1980s.
Saying the estimates were now probably "appreciably lower", the scientific committee said it could not provide any reliable estimates of current minke abundance in the region.
Cassandra Phillips of the World Wide Fund for Nature, who is at the IWC meeting in Adelaide, said that minkes faced increasing threats of other kinds as well - marine pollution, entanglement in debris, and climate change.
"We hope this renewed uncertainty over whale numbers will encourage Japan to recognise the proposed southern ocean sanctuary, and to end its whaling there."
Cassandra Phillips told BBC News Online: "We think this is very significant. The Japanese have been bandying around this figure of three-quarters of a million minkes, but now there's really authoritative evidence that it's totally unreliable.
"It throws into even more question the scientific whaling that's taking place now."
Killing permitted
Japan plans to catch 540 minkes in Antarctic waters this year, using an IWC rule which allows unlimited catches of any species so long as the whales are killed in the name of scientific research. The whalers acknowledge that many people in Japan like to eat whale meat.
Norway, the only country apart from Japan that continues to hunt whales, plans to kill 655 North Atlantic minkes this year. It objected to the IWC's moratorium on commercial whaling, in force since 1986, and so is allowed to ignore it.
The IWC scientific committee's disclosures about the extent of Soviet whaling several decades ago may help to explain why some species are recovering only very slowly from the mass slaughter of the commercial era.
In those days, the IWC assigned members quotas of the whales they were entitled to catch. In the 1959/60 season, the committee says, the Soviet fleet had a quota of 720 humpback whales in the southern Pacific.
It actually caught almost 20 times as many - a total of 12,945 humpbacks, roughly the number thought to survive today in the entire Southern Hemisphere.
Among changes in the list of recognised cetacean species, the committee recommends accepting that there are three species of right whale, not the two recognised today. It says the reduction of deaths caused by human activity among northern right whales should be a priority.