There has been an increase in demand for the work due to a shortage of international cleaning facilities and stricter biofoul thresholds.
Just last week, cruise ship Viking Orion chose to leave New Zealand waters to be cleaned when it only gained restricted port access due to the algae levels on its hull.
Despite the restricted status, the ship still visited commercial ports in Dunedin, Christchurch, Wellington, Napier, Tauranga and Auckland.
Bay Underwater Services, based in Papamoa, has cleaned hundreds of vessels in the past few years - including cruise ships.
Company owner Robert Campbell said they were treated the same as any other ship, but cleaning had drawbacks for passengers.
"It's going to interrupt their travel plans for their cruise, and that's a major for anyone who is paying for a cruise. They're sitting bobbing 'round the ocean while we clean for them."
"There's a lot tied up in doing hull cleaning on vessels that size. You've got to have a good work vessel to start with to work off and do work on a ship.
"We're probably 30 to 40 nautical miles offshore from the Tauranga entrance. The weather conditions out there - we need it to be glassy and calm."
The ships had to be cleaned out of New Zealand territorial waters, or at least 12 nautical miles offshore, often at a depth of 500 or 600 metres.
Auckland-based Commercial Dive Specialists managing director Brook McRae said the deep water was critical to kill the species being removed.
"If that cleaning was done right up on our coast, then those species would take hold, like some of them [already] have," he said.
"We've got these little, small mussels that aren't like the ones we have here … they're in about 75mm-thick carpets and there's hectares of them in some of the west coast harbours now."
Biosecurity New Zealand environmental health manager Paul Hallett said biofouls were not removed lightly either.
"The way they clean is, they actually smash the organisms that are on the outside, so it's not like they gently peel them off. They have chisels and hammers and they break them all apart," Hallett said.
"They've got quite an effective way of killing these things."
Biofouling could happen quickly and randomly, he said.
"It's not one place, one operator. Sometimes it has actually occurred to operators that are doing the best that they can.
"It's because of one particular issue or storm they weren't able to go that extra bit [to check their ship complied]. There's no predictable pattern."
Compliance was usually pretty good, but this season there had been hurdles.
"There are very few places where you can clean, so most operators do in-water cleaning and even then, there are limited areas where you can actually do that. There's also an overload in dry docks, in terms of the amount of ships wanting to dry dock, we understand."
Sometimes there was still a misunderstanding about what was required from ships too, he said.
If the stricter threshold for biofouls had not been introduced, Commercial Dive Specialists' Brook McRae believed the situation would be very different.
"Those ships would have docked in New Zealand, no one would have been the wiser and in a couple of years' time, we would have seen the impact of these new invasive species spreading out," he said.
"I think we've already seen the benefits [of stricter thresholds] just by [Biosecurity NZ] turning around these ships."
Hallett said Biosecurity NZ was going to review challenges faced by cruise ships at the end of the season, with a report expected by the end of June.
