Police officials confirmed on Tuesday that they have opened an inquiry into how faeces ended up in the cans at the Hellenic Bottling Company factory in Lisburn, Co Antrim, reported the Guardian.
Coca-Cola suspended night-time processing last week at the plant when machines became clogged.
The soft drinks giant said it impounded all the affected cans and that the contamination did not affect any products that were on sale.
According to the Belfast Telegraph, factory workers on the night shift at the plant in Lisburn last week were left horrified when they made the discovery inside a number of cans on the production line.
"It was absolutely horrible, and the machines had to be turned off for about 15 hours to be cleaned," a worker told the paper, adding "it was unusual because normally the cans come from somewhere else in the UK, but this time they apparently came from Germany".
In a statement, the company told the newspaper: "Coca-Cola takes the safety and quality of our products extremely seriously."
"We are aware of an incident involving empty cans at our plant in Knockmore Hill, Lisburn. We are treating this matter extremely seriously and are conducting a thorough investigation in co-operation with the police."
"The problem was identified immediately through our robust quality procedures and all of the product from the affected production 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 none of the cans contaminated with faeces had reached the market in Northern Ireland. It added: "The incident is subject to an investigation by the PSNI (Police Service of Northern Ireland) and the environmental health unit of Lisburn and Castlereagh city council."