For more than 200 years, the unexplained deaths of hundreds of Australian Aborigines at Sydney Cove in 1789 have been blamed on an outbreak of deadly smallpox.

Canberra's Australian National University heard on Wednesday that the deaths were not caused by the serious contagious disease, but were the result of the spread of a childhood case of chickenpox.

Sydney University associate professor John Carmody used an address to the ANU Centre for Aboriginal Economic Policy Research to argue it would have been impossible for smallpox to have been present in the fledgling colony, less than two years after the arrival of the First Fleet.

''There is absolutely no evidence to support any of the theories and some of them are fanciful and far-fetched,'' Dr Carmody told Fairfax Media.

''Chickenpox got into the colony because every colonist had it as a child. I think what happened was that children in the colony got it … then played with Aboriginal children and the virus got into the Aboriginal population.''

Dr Carmody also argued theories put forward by academics, including former ANU historian Noel Butlin, that British colonial surgeons deliberately introduced smallpox to wipe out the indigenous population are without foundation.

''I think that is a very serious charge to make and it seems to me that there is no evidence for it whatsoever and you have to finish your diagnosis before you make your claim,'' he said.

Chickenpox was historically considered to be a mild form of smallpox, with the distinction only defined by English physician William Heberden in 1767.

Dr Carmody said communities without immunological resistance to chickenpox could see a death rate as high as 20 per cent.

''We don't know what the mortality was because we don't know the actual number of Aboriginal people who died or very well what the population was,'' he said.

''It was clearly very severe and we know that even in counties like Australia, England and the United States today that if you miss out on chickenpox as a child and get it as an adult, it can be extremely serious and even fatal.''

If the disease was smallpox, Dr Carmody said at least 50 colonists would have died.

''Some dead bodies were brought in from the beaches around Sydney Harbour and surgeons did post-mortems on them, and some sick people were taken in by colonists and nursed but not a single colonist got the disease,'' he said.

Dr Carmody said he hoped the lecture would end suggestions of a kind of ''biological warfare by the colonising powers''.

''Everything I have read in the diaries and journals of the surgeons who came out with the First Fleet leads me to believe that they were very capable medical people within the limits of their training and medical knowledge of the time,'' he said.

''They all struck me as being of really ethical character and I simply can't believe any of them would do that.''