The Southern Discovery underwater observatory partially sank when it was damaged a month ago.
The observatory in Harrison Cove allows visitors to descend 10 metres to view coral, fish and anemones but it has been out of action since the storm.
Southern Discovery said the visitor section had now been safely towed across the sound to undergo repairs.
"The recovery was a delicate operation – acknowledging both the remote location, the sensitivity of the area, and ongoing weather events in September which restricted access to Milford Sound."
All three damaged pontoon buildings were refloated before being moved and secured on shore at Deep Water Basin.
They would now be taken apart and moved from Milford Sound for repairs.
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".
