Like many others, he is concerned at a lack of progress ahead of a crucial UN climate summit in Copenhagen in December.
If there is no deal some time in the next year then there is a risk of momentum fading and the problem getting beyond the reach of world leaders, said Prof Flannery, who is in New York for climate talks.
"My greatest fear is that once people stop negotiating, once diplomacy fails, that's potentially a prelude for war."
That could mean conflict over carbon tariffs, over the mass migration of climate-affected people or over serious water shortages, Prof Flannery said.
It might not happen for decades but it was a real threat if Copenhagen failed. "The triggers are there for conflict," the former Australian of the year said.
He gave some support for Australia's proposal to go easier on developing countries in the Copenhagen process, by exempting them from having to make economy-wide commitments to restrain emissions growth.
The Greens say the plan is a cop-out but Prof Flannery said it should be looked at because current approaches were not working.
"It does hold the promise at least of unlocking further cooperation from those so-called developing countries," he said, adding that countries like China and Brazil were not really developing countries any more. "We haven't got time to let the perfect be the enemy of the good."
Prof Flannery strongly backed Australia voting in its emissions trading scheme before Copenhagen. The Opposition wants a vote delayed.
But Prof Flannery also said Australia must cut emissions by at least 25 per cent. The Government's target is a 5 to 25 per cent cut.
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