Recreational and commercial vessels, including cray fishers' boats, especially if they were laying pots, were equally at risk of unknowingly picking up Undaria on pots, ropes and other gear.
The two harbours were home to the only known populations of "this opportunistic kelp" in Northland, and the challenge was to contain it and keep it out of other harbours in the region.
Mr McKenzie said that would be no easy task, as vessels based in the Bay of Islands often travelled to and from Houhora and Rangaunu, while numerous commercial fishing vessels operated out of Houhora.
"Some of these vessels could well travel to the abundant waters around the Three Kings Islands (Manawatawhi), heightening the biosecurity risk to this high-value marine ecosystem," he said.
"The council, and the wider community it represents, is reliant on boaties to be vigilant and act responsibly to ensure our marine environment is protected from invasive pests. I can't stress this enough — we really do need vessel owners to clean their hulls before they leave Rangaunu and Houhora harbours."
Cleaning with a soft cloth would suffice for vessels with no more than a slime layer, but anything more than that, such as evidence of actual Undaria growth, should be reported to the council, which would work alongside vessel owners to deal with the problem on a case-by-case basis.
The NRC, along with a number of other regional councils, had also introduced a multi-pronged 'Clean below? Good to go' summer awareness-raising campaign (go to www.marinepests.nz for more information).
"The inspection of a planned 2000 boat hulls in Northland over summer has been under way since late last year, and divers are due to begin vessel inspections in Houhora Harbour later this month," Mr McKenzie added.
The council was also in the process of adopting a new Marine Pathway Plan that would introduce new rules on hull-fouling to prevent the spread of marine pests.
The guidelines would call on boat owners to:
* Notify the Northland Regional Council if they found Undaria or other marine pests on their hulls, and not to try removing them themselves;
* Clean their hulls regularly, and keep fouling growth to no more than a light slime layer that could be removed with a soft cloth;
* Apply anti-fouling paint, ensuring all 'niche' areas such as the base of the keel and any hard-to-access places are coated and kept in good condition;
* Make sure the hull is clean and free of fouling before travelling to a new region;
* Clean and dry marine equipment such as ropes, lines or pots before using them in a new location;
* Inspect areas that retain sea water, such as live bait tanks, in case they're harbouring marine life;
* Check anchors, trailers and other equipment for tangled weeds.
* Information on a variety of marine and land pests can be found at www.nrc.govt.nz/pestcontrolhub