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It has already received 133 reservations - 15 fewer than in the 2018-19 season.
Regional harbourmaster Lyndon Cleaver said it was important to consider issues associated with increasing cruise ship visits.
"We have a system for Bluff, Milford Sound and other small ports but we have nothing for the rest of Fiordland and Stewart Island. And these areas are unique."
Mr Cleaver said that work had started last week on a process to manage possible risks.
However, he believed the team would take up to four months to complete the programme, as Southland had a big coastline.
"We still have a long way to go, as we need to identify what are the risks and the best way to mitigate them."
A review of maritime functions and capability would be run concurrently with the Fiordland Safety Management System work, to identify whether Environment Southland had adequate maritime resourcing available to meet future work programmes.
A $179,000 harbourmaster's vessel was being built to ensure the team had the right tools to conduct the work.
Mr Cleaver said the old vessel, Toroa, was quite small - almost a "tub" - and would not be appropriate to use in Foveaux Strait.
However, it could still be used in the southern lakes.
"To maintain the standards of the SMS, you can't do it short-sighted. You need to get out there and this is only possible with a bigger vessel."
Another focus would be managing the number of cruise ships in the Fiordland and Stewart Island region, to protect the environment. The limit now was three cruise ships a day.
"Each year, we have more cruise ships than previous years. It is a good thing, of course, but we need to take care of nature. It is our priority."