Inspectors will visit the UK dairy sector in November, the Commission said, warning that "fundamental differences" existed between its interpretation of the rules on antibiotics in milk and that of the UK Food Standards Agency (FSA).
If there is no agreement on how rules should be enforced then the Commission may have "no choice" but to take legal action against the FSA, a spokesperson told DairyReporter.com
The news comes only days after EU member states banned curd cheese produced by Bowland Dairies in northern England, following Commission concerns over antibiotics in the firm's milk supply.
Its initial inspection at Bowland in June found a range of problems, from cheese containing floor sweepings to contaminated milk. A follow-up visit in September found "there had not been sufficient progress" on the antibiotics problem.
A report on the September inspection will be passed to the FSA today.
June's inspection found Bowland was holding milk already found to contain antibiotics, but waiting up to 13 days to do a second, quantitive test. Milk containing antibiotics residues within the specified EU limit can be used can be used to produce cheese.
"The correct procedure would be to discard the milk, as is the normal practice in the other 24 member states, or to move to a second screening test immediately," said Commission spokesperson Philip Todd.
"We certainly don't consider that the FSA has taken the necessary corrective action". He said the Commission had no evidence there were problems elsewhere in the UK dairy sector, but now wanted to check.
FSA officials rejected accusations they had not acted appropriately. "They still haven't shared that report with us, we don't know what the full claims are. From our own investigation, we haven't found anything," said an agency spokesperson Friday to DairyReporter.com.
Bowland and industry body Dairy UK also rejected the Commission's findings.
Ed Komorowski, Dairy UK's technical director, said there was considerable confusion over the Commission's position on testing for antibiotics in milk.
He said Bowland's 13-day timescale was "ancient history" and that the firm was testing milk on arrival and, if that was positive, then conducting a rapid, three-hour quantitive test.
Bowland said it had been the innocent victim of a dispute between the Commission and FSA.
It recently won a case against the Commission in the European Court of First Instance over the issue of antibiotics residues in its milk. The court ordered the Commission on 12 September withdraw a food alert warning that Bowland produce was unsafe.
The firm pledged to fight again in the courts if the Commission continued to press the issue.
Komorowski 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."
An EU-wide meeting on testing antibiotics in milk is scheduled for 18 October.