The minister and guests took a short boat trip around the fiord, cruising past the foot of Mitre Peak before visiting the centre and unveiling a plaque.
"Milford Sound and the Fiordland National Park are really exceptional and it's good to be reminded just why so many visitors flock here from all around the world," she said.
Ms Wilkinson paid tribute to Southern Discoveries and its partnerships with the Department of Conservation and the Fiordland Conservation Trust.
"Southern Discoveries don't just talk about conservation, they actually do it with the Sinbad Sanctuary project."
At the opening ceremony, Ms Wilkinson experienced the newly developed Milford Discovery Centre, which incorporates Milford Deep, New Zealand's only floating underwater observatory.
The $500,000 development is the only one of its kind in the Piopiotahi (Milford Sound) Marine Reserve, where visitors descend more than 10m below the surface to view marine life in its natural habitat.
Southern Discoveries general manager John Robson said the company had strong conservation values and it was important visitors to Milford had a "learning element" to their experience.
"The new centre is a very innovative way to help people really appreciate this exceptional place.
Among guests at the opening were Doc southern conservator Barry Hansen, Southland District Mayor Frana Cardno, agents and activity operators from Milford Sound, Te Anau and Queenstown, and members of the board of Skeggs Group Ltd, Southern Discoveries' parent company.
