The New Zealand Cruise Association wants the government to help build safe cleaning facilities to reduce the number of cruise ships barred from entering the country's waters.
There is currently no large dry dock for cleaning in New Zealand.
Last season, 11 cruise ships were issued a notice of direction for having biofoul build-up on their hulls, restricting some from going to environmentally sensitive areas like Fiordland.
Biosecurity New Zealand Northern Regional Commissioner Mike Inglis said evidence had found almost 90 percent of the exotic species already here likely arrived clinging to a ship's underside, which was why the standards were strict.
"It's a mixture of pests and diseases and that build-up of high-risk organisms can impact our economy, our marine growth," Inglis said.
Cruise Association chief executive Jacqui Lloyd said lost knowledge of the biofoul standards during the pandemic and limited cleaning options were key factors last season.
Biosecurity NZ and Cruise Association had been educating cruise companies on the standards in the off season and encouraging ships to get their paperwork in early.
Northern Hemisphere ships were now being cleaned in safe facilities in Singapore and Indonesia on their way to New Zealand, Lloyd said.
But Southern Hemisphere ships were still running into trouble, because their only option was in-water cleaning, out of Aotearoa's territorial waters.
"For the ships that have been based in Australia and New Zealand over the winter, there are no safe cleaning facilities in Australasia for ships to be cleaned, so the cruise lines are really at the mercy of the weather," Lloyd said.
"We certainly do not want biofouling in our waters, we want to make sure New Zealand waters are safe and clean, but we need to make sure that if we're putting rules in place, we allow areas for cleaning to take place."
It wasn't just cruise ships affected either - freight, commercial and even the Interislander also had to be cleaned overseas or off the coast, in deep water.
The industry wanted to explore more options with the backing of the government, Lloyd said.
"There are other ways to clean with divers, where they have areas that they can come into and use catch bags and a number of other things to catch whatever is falling off the ship. I think those are areas that we'd like to investigate further until a dry dock is an option."
So far, just one cruise ship had been issued a notice of direction for failing biofouling assessments this season.
"They did attempt to clean, I do want to state that, they were extremely focused to try and do that, but, because of poor and adverse weather, they weren't able to, so they decided to cancel the trip and ended up going elsewhere," Inglis said.
Lloyd said this year was set to be New Zealand's biggest cruise season to date, with about 360,000 passengers, 149,000 crew and more than 1000 port visits planned.
"[If a ship fails to meet the standards], it's thoroughly disappointing for the passengers on board who are wanting to come and experience New Zealand, and thoroughly disappointing for the regions that are expecting that economic benefit," she said.
"Often too, it's a lot of our smaller regions that don't necessarily see a huge amount of international visitation and international visitor spend and that's really important to those local businesses."
Inglis said the season had got off to a positive start, and the vast majority of cruise partners were doing the right things.
"We continue to thank them for the work that they do in this space. We all want to make sure that people can visit a beautiful country and it remains so for future generations."