Machines at the factory in Lisburn, close to Belfast, became clogged up by a container of cans during a night shift last week.
When workers checked to see what the issue was, they found what appeared to be human waste in several cans that had been shipped form Germany to be filled with the fizzy drink.
A source told the Belfast Telegraph: “It was absolutely horrible, and the machines had to be turned off for about 15 hours to be cleaned.
“It was unusual because normally the cans come from somewhere else in the UK, but this time they apparently came from Germany.”
The source said that the rumour is several immigrants made a long journey inside the lorry transporting the cans and used them to go to the toilet.
They added: ”It’s really shocking – and beyond the shock of finding something pretty disgusting in the cans is the thought there could have been poor people in that situation.
“And if they did make that journey, where are they now?”
A Police Service of Northern Ireland (PSNI) spokesman said they were investigating the incident.
A spokesperson for Coca-Cola said they were aware of the incident at the Knockmore Hill plant.
They said: “We are treating this matter extremely seriously and are conducting a thorough investigation in co-operation with the PSNI.
“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 there was no evidence to suggest any affected products had reached the market.
Top pic: Rex/stock photo