Southern Discoveries had an observatory building at Harrison Cove in the sound which let tourists drop 10m beneath water to observe fish and other sea life.
It also had a kayaking pontoon beside it.
A severe storm is believed to have sunk the main building into the sound.
Environment Southland said in a statement yesterday marine and compliance staff visited Milford Sound to inspect the Southern Discoveries building.
Staff from council compliance and marine maritime teams were on site at Milford Sound to inspect the site and liaise with the building owner, Southern Discoveries, on their recovery plan.
Acting regulatory services general manager Bruce Halligan said Environment Southland was very aware of the ecological and cultural importance of the area.
"We are reasonably comfortable Southern Discoveries have secured the damaged structure as best they can to prevent it from detaching and becoming a navigation safety hazard", he said.
"There is a low chance of an oil spill as any contaminants have either been removed or contained for removal once it is safe to do so. Oil spill sorbent booms are in place as a preventive measure."
Environment Southland was notified on Monday that a 200-tonne structure in Milford Sound held up by steel pontoons had sunk below the water surface in bad weather.
It has since been liaising with Southern Discoveries about their recovery plan.
"An update from the company on Thursday was that 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. Southern Discoveries has advised there has been some debris lost into the water and divers will be inspecting the area as soon as conditions permit."
A salvage company has been engaged to remove the damaged parts of the building and recover anything they can from the sea floor next week.
"We are satisfied with the current arrangements to mitigate environmental risks and to secure the facility for navigational safety, and appreciate the constructive engagement with Southern Discoveries. However, we will be maintaining a strong ongoing watching brief to ensure the risks to the environment are being appropriately mitigated and managed."
Chief executive Kerry Walker could not be contacted yesterday.
She told Stuff initial assessments showed the main reception area pontoon was partially submerged.
The main docking pontoon and generator pontoon were visibly leaning, but the underwater chamber and kayaking pontoon were unaffected.
Ms Walker said there had been negligible fuel leakage, of less than 10ml, which dissipated within 30 minutes or was captured.
The observatory building is accessible only by boat.
