Legal action was necessary, the European Commission said, because the UK Food Standards Agency had not sufficiently tackled safety and hygiene lapses found at Bowland Dairies in northern England.
The start of legal proceedings escalates the row between UK and Commission food safety officers over testing for antibiotics in milk, causing confusion for dairy firms.
The Commission said it was particularly concerned that UK authorities were allowing milk containing antibiotics to be used in dairy processing, without first checking whether the antibiotics content exceeded the EU safety limit.
Curd cheese made by Bowland was banned across the EU last Friday, after a second Commission inspection in three months found ongoing problems with antibiotics in its milk.
A report of the second inspection, done in September, had still not been passed to the UK Food Standards Agency (FSA) this Thursday, however. "We have been asking for it," an FSA spokesperson said, adding, "from our own investigation, we haven't found anything".
Fundamental differences existed between the Commission and FSA interpretation of the rules on antibiotics in milk, a Commission spokesperson told DairyReporter.com.
"They [FSA] may not have seen the report but they're fully aware of the situation. We have had extensive discussions with the FSA and other member states."
He added an inspection in June found Bowland was holding milk already found to contain antibiotics, but waiting up to 13 days to do a second, quantitive test. Correct procedure would be to either throw the milk away or do a second test immediately.
UK authorities have five days to provide a satisfactory response to accusations of its negligence, otherwise the Commission will refer the dispute to the European Court of Justice.
Confusion has grown in the UK dairy industry this week, amid concerns it has been unfairly caught up in EU-UK mudslinging.
Bowland, which faces an uncertain future following the ban, pledged to fight. It recently won a case on the same issue against the Commission in the European Court of First Instance.
Ed Komorowski, technical director for industry association Dairy UK, said the Commission position on testing for antibiotics in milk was far from clear.
He said testing for antibiotics in milk varied in the UK depending on whether milk was produced in-house or bought in from outside suppliers. "The industry is open to inspection at any time. We are inspected regularly and we do not see that there is anything wrong."
Commission inspectors will visit several UK dairies in November to check on antibiotics and hygiene standards.