The night shift at the Lisburn factory was disrupted last week when machines became clogged; Coca-Cola said it had impounded all affected cans.
The company stressed this was an isolated incident that did not affect any products currently for sale.
Police are investigating reports that a consignment may have been contaminated.
As reported in the Belfast Telegraph, the cans arrive at the plant without tops on and are then filled with the drink before being sealed and sold across Northern Ireland.
"Detectives are investigating an incident at commercial premises in the Lisburn area following reports that a consignment of containers delivered to the premises had been contaminated," said a spokesman for the Police Service of Northern Ireland.
A spokesperson for Coca-Cola said the company was aware of an incident involving empty cans at the Knockmore Hill plant.
"We are treating this matter extremely seriously and are conducting a thorough investigation," said the spokesperson.
"The problem was identified immediately through our robust quality procedures and all of the product from the affected batch was immediately impounded and will not be sold.
"This is an isolated incident and does not affect any products currently on sale."
The Food Standards Agency said: "The FSA in Northern Ireland is aware of a physical contamination incident at Coca-Cola Hellenic in Lisburn. There is no evidence to suggest that any affected product has reached the market.
"The incident is subject to an investigation by the police and the environmental health unit of Lisburn and Castlereagh City Council."
Pat Catney, Social Democratic Labour Party MLA for Lagan Valley, said the incident "beggars belief".
"I am not sure how contamination could have come about," he said. "They are sticklers for hygiene, cleanliness and about contamination.
"We shall have to wait for the police investigation. But it is a state-of-the art factory. I have been around it and this is one of the most professional setups I have ever seen."