Some 45 locals took their last chance to evacuate on Saturday but others chose to stay despite warnings to get out, with sewerage and power turned off due to flood risks.
Most of those who left were flown by helicopter to nearby Doomadgee and then more than 300 kilometres south to Mount Isa.
Footage taken from a helicopter above the flood zone on Saturday showed the town and surrounding areas were already flooded.
Properties, roads and other infrastructure were inundated, with several aircraft shown perched on a rare strip of elevated concrete.
This is Burketown's worst-ever flooding, with the Albert River surpassing the 6.78-metre record of 2011.
The disaster is expected to peak on Sunday, although Superintendent Tom Armitt told the ABC it was unclear exactly when that would be as the water level had already surpassed flood modelling.
"We don't know how much ground will be left if the water continues to peak and cover all the ground," he said on Saturday.
"If we get to the stage where we are having to shift and move people to rooftops, that makes a whole different level of complexity. "
A forecast for severe thunderstorms and rain in southeast Queensland was downgraded on Saturday, but heavy falls are still possible.
Several towns, cattle stations an isolated settlements in the southeast gulf of Carpentaria remain cut off and are relying on supplies sent by air or barge after weeks of torrential rain.
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