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In an effort to encourage tourists to use buses or carpool, Milford Sound Tourism (MST) has been charging $10 an hour in the main car park since the beginning of the month.
MST general manager Tim Holland said the numbers of tourists visiting the attraction increased by 83% over the past five years and a large proportion of these visitors had been self-driving.
The average occupancy for a car visiting the area was 2.1 passengers, he said.
"If this average could be increased, particularly by more passengers choosing to travel in by coach, this would ease the pressure for car parking, and reduce risks on the road through fewer vehicles using it."
MST installed the pay-by-plate system in the main car park, which has 241 spaces. It uses cameras to recognise licence plates.
The 80 spaces in the Deepwater Basin Rd overflow car park continue to be free and visitors will be able to continue to use a courtesy coach transfer.
"We believe that this will go some way to help improve the utilisation of the car parks and address the issues with parking that have occurred over the last few seasons, while helping to encourage more visitors to choose the various coach and cruise options," Mr Holland said.
The goal was to make sure customers had a pleasant experience and Milford Sound continued to be the "star of the show", he said.
Southern Discoveries chief executive Tim Hunter said it was still too early to determine if there had been an increase in customers looking for coach services. He said the company, which is one of the main operators in the area, had increased the number of buses for the season.