An underwater observatory in Milford Sound has partially sunk after being damaged in a storm.

Southern Discoveries CEO Kerry Walker said the tourist attraction in Harrison Cove - where visitors descend 10 metres to view coral, fish and anemones - was damaged last Sunday.

The observatory consists of five interconnected pontoon networks and initial assessments showed the main reception area pontoon was partially submerged, while the docking and generator pontoons were on a visible lean. The underwater chamber and kayaking pontoon were unaffected.

Walker said it had been closed for maintenance and no staff, contractors or guests were onsite at the time of the event, which happened overnight.

Southern Discoveries was working with the Department of Conservation and engineers to contain any debris, secure the site, and establish a recovery plan.

She said the initial priority was to minimise the spread of debris and any potential environmental issues.

"Early indicators are that there has been minimal impact on the Sound or its wildlife. There has been negligible fuel leakage - less than 10ml - which dissipated within 30 minutes or was captured in debris socks around the site."

Environment Southland acting general manager regulatory services Bruce Halligan said staff from its compliance and marine teams were onsite at Milford Sound on Friday to inspect the site and liaise with Southern Discoveries on their recovery plan.

It was monitoring the site closely given the ecological and cultural sensitivities of the area.

Halligan said it had been told the main building was sitting on a rock supported by some of the floating pontoons and that additional chains had been attached between the land and the damaged part of the building.

He understood some debris had been lost into the water and divers would be inspecting the area as soon as conditions allowed.

A salvage company had been engaged to remove the damaged parts of the building and recover objects from the sea floor next week.

Main image (RNZ/Supplied/Southern Discoveries): The Southern Discoveries underwater observatory in Harrison Cove, Milford Sound has begun to sink following a storm.