One of New Zealand's most treasured tourist spots has received a multi-million dollar cash injection to build flood protection.

Tourism operators in Milford Sound have had to put off redeveloping the area for years because of the risk of flooding and they say the government's $13 million is long overdue.

Kayaking in Deepwater Cove may be a world class experience but the same could not be said for the changing rooms.

"It's a little bit rustic for some people's liking," says Rosco Gaudin from Milford Sound Sea Kayaks.

Permanent buildings have been put on hold for over a decade because the area is considered too high a flood risk. The original accommodation was built for around 70 staff but has to hold nearly three times that.

With an average rainfall of eight metres a year, Milford Sound is more prone to flooding than most and the main road, airstrip and land that used to be in the river's path is most at risk.

But Conservation Minister Steve Chadwick has now announced funding for flood mitigation protection.

"It's held development up here for years...in 1972 they started to point out the level of risk and started to realise it. This has escalated more and more when we've got these extreme weather bombs that we're seeing," says Chadwick.

The only flood protection in the area is nearly 30 years old and designed to withstand a one in 50 years flood which is no longer adequate.

The $13 million will buy a bigger wall and should withstand a one in 100 year flood.

"We've been waiting 10 years for some action to be taken on this stopbank...it's better late than never but it's definitely long overdure," says Gaudin.