Scientists believe stem rust, which looks like red dust on wheat, could threaten global food security.
A new strain of the disease is spreading throughout eastern and southern Africa and researchers say it could arrive in Australia on high winds.
Researchers are racing for ways to protect vital food crops and have just been given a $40 million boost from the Bills Gates Foundation.
Grains Research and Development Corporation (GRDC) chair of cereal rust research at the University of Sydney, Professor Robert Park, says stem rust has the potential to kill wheat crops.
He says there is one particular variety of wheat rust which is proving difficult to stop - UG99 - found in Uganda in 1999.
Twelve years on, UG99 has moved into southern Africa.
"Now we know from our long-term work at the University of Sydney that there was one incidence at least, in the late 1960s, where stem rust was transported from southern or central Africa to Australia by high-altitude winds," Professor Park said.
"This now means that we're pretty much in the firing line.
"In 1973 we had a single epidemic of wheat stem rust in south-eastern Australia, and at that time the damage bill was estimated at something like $300 million. There were crops that were actually killed.
"So you can gauge from that the potential for this disease to cause destruction.
"The added significance of UG99, this new race of stem rust, is that it overcomes pretty much all of, or most of the genes that have been resistant that have been bred into wheat by wheat breeders over the past 50 years."
Professor Park says testing of UG99 on Australian wheat germ has produced worrying results.
"We've had Australian wheat germ plasma tested in Kenya against UG99. We know many of our current varieties are susceptible," he said.
"One of the ways of minimising that risk would be to control that rust pathogen in southern Africa to keep the rust inoculant levels low, so by assisting farmers in that part of the world and in east Africa indeed to control this rust, it's reducing its potential to spread."
The new funding from the Bill Gates Foundation will be used for field sites, operational greenhouses and other critical infrastructure in Africa.
Professor Park says new stem rust-resistant wheat varieties need to be developed and their seeds need to be distributed as rapidly as possible.
"A large part of this project is about developing capability in the developing world and that's what it's all about, helping people to provide for themselves," he said.
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