Clint Tauri applied to Environment Southland last year for a new coastal permit.
For the past 10 years, his company Fiordland Cruises Ltd offered back-country charter trips in the area and, from mid-February to the end of June last year, was temporarily allowed to operate day trips while the Milford Rd was closed.
He had wanted this to continue, and asked at a hearing in March for commissioner Sharon McGarry to consider the need for his company to survive in the face of global travel restrictions over the next three to five years.
She refused it, however, saying the environmental effects of the application could be more than minor.
She also said, while it was considered, concern from Mr Tauri that one company effectively held all of the day trip allocation was not relevant.
Concerns had also been raised by Environment Southland consents officer George Gericke that there could be cumulative effects on remoteness and wilderness values if approved.
This was one of the points Mr Tauri was against in his appeal, which was submitted to the Environment Court on April 16.
He sought an order to set aside the decision and for the consent to be granted.