Yachting New Zealand may find itself about $100,000 out of pocket after its appearance before the Sports Disputes Tribunal and the Court of Arbitration for Sport.
Chief executive Simon Wickham said the tribunal process and decision had cost Yachting NZ $50,000 in legal fees.
The final cost of the arbitrationcourt appeal had still to be worked out, but he estimated it would also be about $50,000.
"That doesn't account for any of the time involved by the staff," Wickham said.
"The selectors have taken numerous hours out of their personal lives, at a personal cost, to prove themselves right."
Most disappointing was the cost incurred by the sailors originally nominated, he said.
"For example, Hamish Pepper had to get himself up to Europe at very short notice. Because he is not an appellant - he was an interested party - they don't have the ability to seek costs."
The court had yet to rule on the matter of costs.
"The difficulty is you have to make a case to seek costs from the sailors concerned [Andrew Murdoch, Simon Cooke and Alistair Gair], which is an option we will consider."
Wickham said the $100,000 had come out of Yachting NZ's Olympic preparation fund.
"Every dollar spent there is a dollar that could have been spent preparing sailors for the Games and that is the unfortunate thing."
Eliminating lawyers from the tribunal process could be a way of reducing costs, he said.
Yachting NZ had nominated Laser sailor Pepper and 470 sailors Andrew Brown and Jamie Hunt after they won the Olympics trials.
But Murdoch, who finished second to Pepper in the trials, and 470 sailors Cooke and Gair, who were third in the trials, appealed to the tribunal, arguing that the chosen trio's results had not fulfilled one of Yachting NZ's criteria, that crews had to show they could finish in the top 10 in Athens.
The tribunal upheld those appeals and told Yachting NZ to reopen the nomination process for those classes, directing the Laser sailors to compete in next month's world championships in Turkey.
Yachting NZ appealed to the arbitration court, which overturned the tribunal's decision, allowing the original nominations to stand.
Wickham said the tribunal "is going to have to sit down and have a long, hard look at the decision it made and the decisions it makes in the future".