Tests on three samples of Benna milk established the presence of a slight bacterial contamination, although health authorities insisted this was not harmful.
The locally produced milk came under scrutiny last week after people complained it had turned sour before the expiry date.
Although Malta Dairy Products was quick to say tests established there was nothing wrong with the production batch in question, an investigation by the Environmental Health Department found that three samples were contaminated with Enterobacteriaceae.
Enterobacteriaceae is a large family of bacteria that includes the commonly known salmonella and E-coli.
Department director John Attard Kingswell told The Times the levels of the bacteria were very low and would not be dangerous to anyone who drank the milk.
The department said the milk was not rendered unfit for human consumption.
One of the samples was taken from a retailer on August 17 while the other two were taken from the MDP's factory the following day.
The department was unable to determine where the contamination came from. Mr Attard Kingswell said it could have come from source since pasteurisation did not sterilise the milk, or through the distribution. He said since complaints had come from different localities, it was unlikely the fault lay with retailers.
The six complaints revolved around milk bought from eight outlets in Birkirkara, Żejtun, Fgura, Senglea, San Ġwann and Swieqi.
In a statement issued yesterday afternoon, the department said it regularly performed market surveillance to ensure highly perishable items, like milk, were being kept at optimal temperatures.
Almost 600 inspections of retail outlets and milk distributors were carried out this year, and in 10 cases it was found the milk was not being kept at the right temperature and destroyed.
Mr Attard Kingswell said milk had to be kept at a temperature below eight degrees Celsius and customers should ensure it was properly refrigerated before buying it.
The department has informed the Veterinary Regulation Fisheries Conservation and Control Division of its findings. The division is responsible for the monitoring of the production plants of food of animal origin.
In a comment posted on timesofmalta.com, MDP quality assurance manager Stefan Mifsud said the presence of any particular bacteria in the milk did not explain why it turned sour before the use-by date.
He said European legislation accepted the possibility that pasteurised milk might have a slight content of Enterobacteriaceae at the end of the manufacturing process, adding pasteurised milk naturally contained various bacteria, which was why these products had a short shelf life.
"This allows the milk to be called fresh and differentiates the product from sterilised products, much like fresh fruit is different from canned fruit. The fact microorganisms are still present in fresh products is the reason why they need to be kept refrigerated at all times. The shelf life of fresh milk is tied to refrigeration temperatures and must be abided with at all stages if the intended shelf life is to be achieved," he said.