A cleaning operation is up and running at Cadbury's Marlbrook plant in Herefordshire to ensure no salmonella remains at the plant.
Cadbury will increase its contamination testing levels
The firm had to recall one million chocolate bars in June when flaws were discovered in its methods of testing.
Herefordshire Council's investigation results showed all samples tested negative for the bacteria.
Cadbury had blamed a leaking pipe for the salmonella contamination at the factory, near Leominster.
Cadbury agreed to improve its contamination testing and thoroughly clean its production lines after meeting with the Food Standards Agency (FSA) on Thursday.
Andy Tector, Herefordshire Council's head of environmental health said: "The cleaning operation which was agreed between Cadbury's, Herefordshire Council and the Food Standards Agency is effectively a belt and braces to reassure us there is no possibility salmonella will remain in the system."
The clean-up will take several months to complete as it requires engineering work to be undertaken and a complete dismantling of equipment.