An outbreak of salmonella has closed part of Fonterra's Hautapu dairy factory for two weeks and seen an entire day's production of milk protein concentrate placed in quarantine.
The concentrate is used in the manufactured products such as cheese and infant formula.
The dairy giant does not know which strain of salmonella has been found at the site and it will be at least two weeks before more tests clear the concentrate factory to resume production.
It will also take that long for Fonterra to find out if the quarantined concentrate can be used, dumped or turned into stock food.
In the meantime, staff at the plant, 4km northwest of Cambridge, are carrying out more testing and a major cleanup, Fonterra's New Zealand manufacturing general manager Brent Taylor said.
The positive test for salmonella was reported to the dairy giant this week.
Mr Taylor said staff, the New Zealand Food Safety Authority and outside auditors were trying to find where it had originated. He expected the testing process to take up to two weeks.
"It is a fairly rigorous process," he said. "When we believe we have found where the problem is, we'll do a complete cleanup before asking permission to begin processing again."
Salmonella is a type of food poisoning and an infection of the stomach and digestive tract.
It is caused by a bacteria found in raw or not fully cooked meat, usually pork or chicken.
Salmonella may be spread by an infected person who works with food.
The positive test was found in product at Hautapu's milk protein concentrate factory, one of six on the site and the only one affected by the outbreak.
Mr Taylor said the positive result had come from the company's own daily testing regime.
The results of daily sampling were available three days after being taken and in that time the product would still be stored on site, meaning it could be stopped from entering the market, he said.
The closure would not create a shortage of concentrate as about 50,000 tonnes were being produced annually at four main sites around the country.
Milk protein concentrate is made by forcing milk through miniscule filters to remove the proteins.
The proteins are then dried to produce a powder that can be used in other manufactured products such as infant formula and cheese.
It is not the first outbreak of salmonella at Hautapu, with another occurring last year, Mr Taylor said.
"It's something we don't want at all," he said.
Fonterra, one of the top ten dairy companies in the world with assets of $4.9 billion, is owned by its 13,000 New Zealand suppliers.