A bee-killing parasite has been discovered at a Victorian shipping port on board a vessel carrying hives, sparking biosecurity measures.

The deadly varroa mite, known to weaken and kill honey bee colonies, was detected at the Port of Melbourne on Wednesday after the arrival of a ship, Agriculture Victoria announced on Friday.

The threat was investigated and treated by the Commonwealth Department of Agriculture, but the state authority has remained in the area to monitor the situation as a "precautionary measure".

Netting has been used at the ports and nearby parkland to contain the bees' movement as the department tests hives.

Initial results of the ship's established beehives were negative for the mites.