The company applied to the Environment Court in March for a waiver to appeal the condition outside the appeal period, saying the number of flights was too restrictive.
Judge Jon Jackson declined the waiver application because it was 14 months late and an appeal against the resource consent by the Arthurs Point Protection Society and resident Barry Walters would be "unduly prejudiced" if the application were granted.
In a decision on costs released last week, he ordered Totally Tourism to pay $1225 to the society and $436 to Mr Walters.
He said Totally Tourism had wasted the court's time.
"These proceedings should not have been brought. The appeal was excessively out of time, with the end result being inefficient use of the court's time, and, that of a voluntary organisation with limited funds," he said.
The consent, granted in November 2008, allowed the company to fly all types of clients to and from the helipad, but landings were restricted to four a day.
The company now wants as many flights as possible without breaching noise standards for the area, which is 11 landings per day, averaged over seven days.
The maximum number of flights a day would be 23.
The company is still operating under its 1992 consent to fly up to 24 daily trips, of rafting clients only, to and from Arthurs Point.
Totally Tourism director Mark Quickfall said he had not decided yet whether to surrender the consent and lodge a new application.
Four daily trips was too restrictive for the business to operate, he said.
"Our wish is to simply operate from the helipad in the same manner, and based on the same conditions we were led to believe were valid under our existing resource consent," he said.
The Arthurs Point Protection Society's appeal will become redundant if the company decides to amend the application and reapply.
If the company continues with the consent, an Environment Court hearing will take place in early October.
