The figure was revised down overnight from 53 to 20.
But Queensland Police deputy commissioner Ian Stewart said on Saturday it had been revised up to 28.
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"There has been some volatility in the number of missing persons," he said.
"Police became aware of a separate list of missing persons compiled by the local council in the Lockyer area overnight, and we've been working hard to reconcile their list against ours.
"Unfortunately, our list has now got a registered 28 persons that we are investigating as missing persons."
The death toll from the floods remains at 16.
The missing are all from Toowoomba and the Lockyer Valley, where a wall of water destroyed homes and buildings on Monday.
Grave concerns remain for 12 people, including 11 from two families at Murphys Creek.
