It could also interfere with boat equipment and aquaculture and affect recreational activities such as diving by changing the underwater character.
The fanworm is considered to be very hard, or even impossible, to eradicate once it is well established.
The fanworm has already been discovered in Auckland, Lyttelton and Whangarei and on barges in the Coromandel earlier this year.
Regional council general manager of natural resource operations Warwick Murray said it was extremely disappointing to find the fanworm in Bay of Plenty waters.
"It's most likely the organism was brought here on the hull of a boat. Boat owners must remember to regularly clean their boat hull, keep their anti-fouling paint in good order, and ensure the hull is clean before they travel to a new region."
Diver and fishing charterer Russ Hawkins said the discovery was concerning, even if it was only a single specimen found. Mr Hawkins said most boaties would typically wash their boats down after being in salt water. It was possible the fanworm could have made its way to the Bay by travelling down the east Auckland channel.
Tauranga Harbour is part of a formal surveillance programme carried out by Niwa on behalf of the Ministry for Primary Industries. The last survey was completed earlier this year and found no evidence of Mediterranean fanworm.
Didymo (Didymosphenia geminata), also known as "rock snot" is a freshwater algae that has inundated South Island rivers and people are legally obliged to prevent the spreading of it. Didymo can be spread by a single drop of water.