Jersey Dairy, based on the Channel Island Jersey, off Britain, said it had recovered around 1,900 of the affected packs of semi-skimmed ordinary and organic milk.
The problem may add to concerns over dairy hygiene in the EU, coming only two weeks after the European Commission filed legal action against the UK for failing to protect the public from contaminated milk at a dairy in northern England.
Kevin Keen, managing director of Jersey Dairy, said: "Overnight tests have shown that there is a higher level of bacteria in this milk than our stringent standards allow. This bacteria may not be harmful."
The firm was investigating how the milk, which had safely cleared pasteurisation, came to be contaminated.
The batches were sent to shops before Jersey Dairy had received results from overnight tests, but Keen added the firm "runs testing throughout the day". He apologised to customers.
"We take this very seriously because we supply milk to the whole island. All the milk produced yesterday has been cleared so it seems to have been an isolated incident," he told DairyReporter.com.
The recall threatens to widen a dispute between EU and UK authorities on testing for contaminants in milk.
Jersey is a British crown dependency. It is responsible for its own food safety, but authorities there have liaised with the UK's Food Standards Agency in the past on EU food hygiene rules.
The European Commission recently filed court action against the UK over concerns the country was allowing milk containing antibiotics to be used in dairy processing, without first checking whether the antibiotics content exceeded the EU safety limit.
Curd cheese from Bowland Dairies, the firm at the centre of the dispute, has been banned across the EU. Commission officials are now set to carry out sweeping inspections of UK dairies from 20 to 28 November.
Both Bowland and the UK Food Standards Agency have rejected accusations of bad practice.