Marine pests in the Southern Hemisphere's second-largest harbour are to come under scrutiny in earnest for the first time in more than a decade thanks to a joint agency survey.

The Northland Regional Council, its Auckland Council neighbour and the Ministry for Primary Industries have contracted marine biosecurity experts from Niwa to carry out the work on the Kaipara Harbour.

The work is weather dependent but is scheduled for May 13 to 24. The last marine biosecurity survey of the Kaipara Harbour was carried out by precursor agencies to MPI in 2006.

The two councils share jurisdiction over the 900-plus hectare harbour and NRC's Kaipara councillor Penny Smart said the new survey is designed to boost knowledge of the current marine pest situation there, especially on and around artificial structures - considered high-risk for pests.

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NRC marine biosecurity manager Amélie Augé said the Niwa team will be looking for a range of marine pests using methods including diver searches, crab traps, seafloor sampling and shore searches.

Cr Smart said survey organisers have already been liaising with some stakeholders including tangata whenua and will be writing to others shortly to advise them of the survey and give an assurance that known scallop beds will be avoided during sampling.

Augé said samples of marine pests - and any other suspect animals or plants - will be collected for identification by taxonomists where their identity is unknown.

The results of the survey will be shared publicly once all collected samples have been identified.

"At this stage, we hope to be able to do this before the end of the year."

Cr Smart said the results will be used as part of a collaborative approach to manage marine pest risks in the Kaipara Harbour by NRC and Auckland Council.

The survey comes as the country's four northernmost regional councils - Northland, Auckland, Waikato and Bay of Plenty Toi Moana - seek public feedback as they collectively consider creating a consistent regulatory approach to marine pests.

For several years the council have been working alongside Biosecurity New Zealand and boaties from all over to stop the spread of unwanted marine pests.

NRC said while Biosecurity New Zealand manages national rules to minimise the risks of new pest species arriving on vessels from overseas, the regulations for vessels moving around within coastal waters vary from region to region.

A number of potential options are being considered.

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