It is safe to microwave milk according to the Dairy Farmers of Canada. It should be done in short increments of time to avoid overheating the beverage.
Milk can be heated safely in the microwave, but, according to Dairy Goodness, it is important to heat the milk on medium or medium-high power and stir it every 15 to 20 seconds. This allows the heat to distribute evenly, permits steam to escape and prevents a film of proteins forming across the surface of the liquid, which creates problems with the texture. The lower microwave power also offers more control over how hot the milk becomes while it is heating.