Sir Macfarlane recommended in a secret report in 1947 that biological and chemical weapons should be developed to target food crops and spread infectious diseases. His key advisory role on biological warfare was uncovered by Canberra historian Philip Dorling in the National Archives in 1998.

The department initially blocked release of the material on the basis it would damage Australia's international relations. Dr Dorling sought a review and the material was finally released to him late last year.

The files include a comprehensive memo Sir Macfarlane wrote for the Defence Department in 1947 in which he said Australia should develop biological weapons that would work in tropical Asia without spreading to Australia's more temperate population centres. "Specifically to the Australian situation, the most effective counter-offensive to threatened invasion by overpopulated Asiatic countries would be directed towards the destruction by biological or chemical means of tropical food crops and the dissemination of infectious disease capable of spreading in tropical but not under Australian conditions," Sir Macfarlane said.

The Victorian-born immunologist, who headed the Walter and Eliza Hall Institute of Medical Research, won the Nobel prize for medicine in 1960. He died in 1985 but his theories on immunity and "clonal selection" provided the basis for modern biotechnology and genetic engineering. On December 24, 1946, the secretary of the Department of Defence, F.G. Shedden, wrote to Macfarlane Burnet saying Australia could not ignore the fact that many countries were conducting intense research on biological warfare and inviting him to a meeting of top military officers to discuss the question.

The minutes of a meeting in January, 1947, reveal that Sir Macfarlane argued that Australia's temperate climate could give it a significant military advantage. "The main contribution of local research so far as Australia is concerned might be to study intensively the possibilities of biological warfare in the tropics against troops and civil populations at a relatively low level of hygiene and with correspondingly high resistance to the common infectious diseases," he told the meeting. In September, 1947, Sir Macfarlane was invited to join a chemical and biological warfare subcommittee of the New Weapons and Equipment Development Committee.

He prepared a secret report titled Note on War from a Biological Angle suggesting that biological warfare could be a powerful weapon to help defend a thinly populated Australia. Sir Macfarlane also urged the government to encourage universities to research those branches of biological science that had a special bearing on biological warfare.

A clinically scientific approach is evident in a note he wrote in June, 1948. He said a successful attack with a microbiological agent on a large population would have such a devastating impact that its use was extremely unlikely while both sides were capable of retaliation. "The main strategic use of biological warfare may well be to administer the coup de grace to a virtually defeated enemy and compel surrender in the same way that the atomic bomb served in 1945.

"Its use has the tremendous advantage of not destroying the enemy's industrial potential which can then be taken over intact. "Overt biological warfare might be used to enforce surrender by psychological rather than direct destructive measures."

The minutes of a meeting at Melbourne's Victoria Barracks in 1948 noted that Sir Macfarlane "was of the opinion that if Australia undertakes work in this field it should be on the tropical offensive side rather than the defensive. There was very little known about biological attack on tropical crops." After visiting the UK in 1950 and examining the British chemical and biological warfare research effort, Sir Macfarlane told the committee that the initiation of epidemics among enemy populations had usually been discarded as a means of waging war because it was likely to rebound on the user. "In a country of low sanitation the introduction of an exotic intestinal pathogen, e.g. by water contamination, might initiate widespread dissemination," he said.

"Introduction of yellow fever into a country with appropriate mosquito vectors might build up into a disabling epidemic before control measures were established." The subcommittee recommended that "the possibilities of an attack on the food supplies of S-E Asia and Indonesia using B.W. agents should be considered by a small study group".

It 1951 it recommended that "a panel reporting to the chemical and biological warfare subcommittee should be authorised to report on the offensive potentiality of biological agents likely to be effective against the local food supplies of South-East Asia and Indonesia". Dr Dorling said that while Sir Macfarlane was a great Australian he was also a product of times when many Australians held deep fears about more populous Asian countries. He said the Menzies government was more interested in trying to acquire nuclear weapons. "Fortunately this also proved impracticable and Australia never acquired a weapon of mass destruction."

The secretary of the Federation of Australian Scientific and Technological Societies, Peter French, said he had not yet seen the files but the whole notion of biological warfare was something that Australian scientists would not be comfortable with today. "Viewed through today's eyes it is clearly an abhorrent suggestion," Dr French said.