Biosecurity New Zealand and the Cruise Association say they are working together to reduce the number of cruise ships being sent for last-minute cleaning.
Over the past month, four cruise ships have been denied entry or given only restricted access to New Zealand ports because of algal build-up or invasive species attached to their hulls.
A joint meeting was held on Monday between Biosecurity NZ and the NZ Cruise Association to address the growing numbers of ships needing extra cleaning when they were already on their way to the country.
Association chief executive Kevin O'Sullivan said an increase in biosecurity inspections may be contributing to the issue.
"Nothing in particular has changed, with the exception that there was probably more inspections being carried out this season because of the gap since ships were here last."
During the pandemic, many ships were docked for months or years - giving algae, barnacles and other organisms the perfect opportunity to grow.
Now, a shortage of international cleaning facilities meant some were missing out on regular cleaning.
Tourism operators were getting annoyed by a string of cancellations as ships missed stops, took detours or postponed trips to be cleaned.
O'Sullivan said the association had sympathy for them, but they weren't the only ones hurting.
"At the end of the day, the cruise lines are losing revenue, they're incurring the wrath of unhappy passengers [as well] ... It's certainly a far from ideal situation."
The issue had to be taken care of and meeting with Biosecurity NZ was a good start, he said.
"The protection of New Zealand's marine environment is critically important for the cruise industry and that's especially true in our most sensitive areas ... We're continuing to work closely with government agencies about any future undertakings and resolve the issues that are happening at the moment."
O'Sullivan believed last-minute cleanings may be prevented if cruise lines were encouraged to begin inspections well before the season starts.
In a statement, Biosecurity NZ said the meeting was "very constructive".
It said it remained "fully committed to balancing the need for cruise visitors to be in New Zealand, with protecting our special marine environment and economy. To this end, Biosecurity New Zealand will continue to work very closely and actively with vessel operators".