Raw milk has not been pasteurised (heat treated) to kill bacteria like E. coli, Campylobacter and Salmonella that are potentially in it.
It was associated with 10 outbreaks that affected 41 people in the country in 2014.
New regulations require registered farmers to sell raw milk directly from the farm gate or by home delivery with a transition period for existing producers up until 1 November 2016.
The agency said people who choose to drink raw milk should make sure they get it directly from the farmer and are only buying it for personal and household consumption.
Other agencies have also warned about the product, the Food Safety Authority of Ireland (FSAI) recommended last year that the sale of raw milk for human consumption be prohibited.
The US Centers for Disease Control and Prevention (CDC) blamed the legal sale of raw milk for a rise in the number of outbreaks associated with unpasteurized milk in 2014.
Matthew Stone, MPI director animal and animal products, said many people who drink raw milk don’t understand the risks or realise that they could get sick from bacteria in it.
“No matter how carefully the animals are milked there is always a risk that harmful bacteria can get into the milk,” he said.
“There is no way of telling by taste, sight or smell if the milk you are drinking contains any harmful bacteria so we recommend that people heat their raw milk until just boiling (or to 70 degrees Celsius for one minute) before drinking it."
Keeping raw milk refrigerated (4 degrees Celsius or less) reduces the risk of bacteria growing to levels which make people sick. People should discard milk if it has been out of the fridge and has reached room temperature.