Wigan Council said two sidewalls on either side of the river were partially washed away.
The River Douglas was badly hit by the recent rain and large sections were flooded.
A crane sited in the car park of the nearby headquarters of bookmakers Tote was knocking the building down.
Council bosses said the single storey building was in danger of collapse.
A spokesman said the owner had contacted the Environmental Agency personally and arranged for demolition contractors to attend.
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