A Fire and Emergency New Zealand spokeswoman said crews from Bluff and Kingswell stations were called about 10.50am today to South Port at Bluff Harbour.
Crews assisted ambulance staff with a Stokes basket, the spokeswoman said.
A St John spokeswoman said one patient was taken to Southland Hospital with serious injuries.
Bluff Marine Radio operator Meri Leask said the incident involved a staff member on the Talleys trawler Amaltal Explorer.
Talleys chief executive Tony Hazlett said the crewman was injured on board the vessel on Wednesday. He was now in hospital in a stable condition.
The trawler was south of Bluff when the incident happened, and the company was undertaking an investigation, Mr Hazlett said.
WorkSafe has been approached for comment.