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45 fire fighters and 9 crews attended the scene at Fenland District Industrial Estate from 5.30pm yesterday.
Residents living close to the site were advised to keep all doors and windows closed because of fumes coming from burning chemicals inside the factory.
Station Road was closed in both directions between Marne Road and Turningtree Road for several hours.
The cause of the fire is not yet known.
No one has been hurt.