His "tentative view" was that Thunder Jet parent company Queenstown Water Taxis Ltd and the Queenstown Lakes District Council were entitled to costs.
The judge said if agreement was not reached on costs, the court would decide.
KJet has already paid $187,500 to Queenstown Water Taxis and $133,000 to the local council in costs after losing a five-year battle to maintain its 10-year monopoly on the Kawarau River.
KJet and Thunder Jet are owned by brothers Shaun and Neville Kelly, who have a long-standing feud.
KJet owner Shaun Kelly said KJet was considering its options from here."It's early days and we're in the process of considering our options now," he said.Thunder Jet director Debbie Kelly, Neville's wife, said they were "absolutely delighted" with the decision.
"You'd like to think this is the end of it all now. It's not us that instigates it but you've got to stand up for yourself.
"We want to concentrate on the future, hopefully they will too."
Queenstown Water Taxis Ltd, the parent company for Thunder Jet, applied to Queenstown's council for consent to operate on Lower Shotover back in 2013.
KJet opposed on safety issues but after various hearings, the Environment Court confirmed the resource consent.
KJet lawyers then appealed. The case centred on whether previous KJet resource consents for that river had lapsed and procedural legal matters.
Shaun Kelly said the companies now had an "integrated safe operational plan" for both rivers.
