60% of Southern Discovery's underwater observatory in Milford Sound is being removed from the fiord for repairs after sustaining critical storm damage at the beginning of September.

Southern Discoveries Underwater Observatory in better days. Three of the five pontoons have now been removed for repair, putting the tourist attraction out of action for some time.

Three of the five pontoons, including the visitor section, have now been towed from their Harrison Cove home to Deepwater Basin for removal and repair.

An Environment Southland spokesperson said that following the storm, the building had been immediately secured and steps taken to ensure against any potential oil spill.

While it had been initally reported that only the visitor section had been damaged, closer inspection revealed three of five pontoon buildings had been damaged.

The recovery had been a delicate operation, due to the remoteness of the location, the sensitivity of the area and ongoing weather events in September which restricted access to Milford Sound.

The three damaged pontoon buildings were refloated and safely towed across the sound late last week before being secured at Deepwater Basin, they said.

The damaged pontoons will now be deconstructed and removed from Milford Sound.

Southland harbourmaster Lyndon Cleaver said New Zealand Dive and Salvage had done a good job managing the recovery and keeping all parties informed of progress.

A Southern Discoveries spokesperson said they did not know how long the observatory would be closed for as they were still in the assessment stage.

Affected staff had been offered redeployment into Southern Discoveries Milford Sound Cruise operation, they said.

Some had accepted these roles while other had chosen alternative employment outside of Milford Sound, they said.