Niwa and Environment Southland recently surveyed the rocky sills that run along some fiords, about 50m deep, as part of an assessment of the 20 areas within Fiordland designated as anchoring sites for cruise ships.
The footage from a remote-operated vehicle captured what Niwa believes are new species and previously undescribed habitats such as rare and protected red coral, sponges and sea pens.
"The scientists were surprised with what is down there. It's pretty amazing," Niwa Nelson area manager Ken Grange said.
"There were several dozens of things that are new to science: sponges, sea pens, corals, sea squirts and sea cucumbers."
There were also large black coral trees which sheltered rock lobsters, he said.
Ships' anchors would be very destructive to those habitats.
Last cruise ship season, 87 ships brought tourists to Fiordland although only a few dropped anchor, he said.
Southland regional harbourmaster Kevin O'Sullivan said cruise ships ranging from 20,000 tonnes to 40,000 tonnes often stopped to take passengers on small boat trips in the fiords and anchored overnight.
The cruise operators had a deed agreement with Environment Southland to anchor in the fiords. Only one cruise ship was allowed in any fiord at a time.
The areas surveyed were beyond the range of divers but the new technology, beginning with sonar studies, indicated there was more to the sills than originally thought, he said.
"We didn't know what was there. There were gasps of 'amazing' and 'wow'."
However, the discovery of the species meant areas where cruise ships had anchored would have to be protected.
"There are areas we would prefer not to use as anchorage but we have identified areas that would be better for them [cruise ships]."
Every year, the council negotiated with cruise ship companies over issues such as anchorage and it was hoped new anchoring areas could be put in place by next cruise ship season.
