The fresh cream had been produced for domestic consumption in the North Island.
Fonterra Brands New Zealand Managing Director Peter McClure said he did not want to speculate on how the contamination occurred.
But he told Radio New Zealand it was unlikely to have come in with the milk from the farms, and it was "almost impossible" the contamination could have been deliberate.
It was the first time in 18 years a Fonterra product had tested positive for E.Coli, which is found in human and animal faeces and can cause infections and symptoms similar to food poisoning.
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That scare turned out to be a false alarm, but French dairy giant Danone announced last week it was suing Fonterra for compensation.
The company, which has since cancelled its supply contract with Fonterra, had estimated the crisis had cost it USD 407 million.
In 2008, six children died and another 300,000 fell ill in China after a local company part-owned by Fonterra illegally laced milk with the chemical melamine.