It pointed out that in other ISAF committees where Spain has representation it had supported retaining the RS:X class.
Boardsailing has been on the Olympic programme since Los Angeles in 1984. An online petition to force a change in the ISAF decision had passed 17,180 signatures yesterday.
The ISAF handling of the issue has infuriated New Zealand's finest windsurfer, Barbara Kendall.
Kendall, now an International Olympic Committee member, but wearing her hat as dedicated allround board sports athlete, believes the procedures used by the ISAF were flawed.
There was a lack of due diligence in the process by which that decision was taken and she believes Spain's declaration that it was confused by the situation may have opened "a can of worms" on the issue.
"What I'm really upset about is ISAF's procedure, the way this happened and its lack of professionalism," she said yesterday.
Kendall, winner of gold, silver and bronze Olympic medals at the first three Games to include women's windsurfing, said the ISAF's approach to selecting Olympic classes looking ahead was flawed, citing the dumping of the Tornado class in 2008, then realising it left the Olympic regatta without a multi-hull discipline for this year.
"The reality is both sports are absolutely fantastic," said Kendall, who participates in both disciplines. "There's no blame on kitesurfing or windsurfing.
"ISAF's procedures in the selection of equipment for 2016 is flawed."
Kendall had issues with the makeup of the voting personnel, pointing to a lack of Asian representation. "Due diligence wasn't done and when you're an organisation responsible for a lot of money and you do make changes that is absolutely essential. From what's been seen it hasn't been done, [and] ISAF loses so much credibility; it's quite sad.
"I hope they will be feeling quite uncomfortable."
Kendall has a solution for the issue. The total number of Games sailing athletes cannot be increased, but some classes could be trimmed in size, allowing both kites and windsurfers to be on an Olympic programme. "You can have a board sports division, separate them from the other classes, create a beach festival, make it more spectator friendly, better for TV and you could have an amazing event," Kendall said.
The issue is now whether Spain's revelation will force the ISAF into reconsidering its decision to plump for kites in Rio, or whether other countries might come forward with similar revelations. Legal action is thought a possible step down the line.
International sports governing bodies are not known for a flexible attitude to changing decisions. The ISAF annual meeting is in November. If the present situation remained intact at that stage, a vigorous case is sure to be mounted by the windsurfing community.
Whatever the personal preference in the two disciplines, the issue has significantly raised the profile of board sports.