10 of the 12 team principals got together on race morning to discuss a range of pressing issues - including the future governance of F1, the rise in entry fees and cost controls.
It comes ahead of a crunch meeting with the FIA and Bernie Ecclestone in Paris on October 23 to try and reach agreement on the future direction of the sport.
Neither Red Bull nor its sister team Scuderia Toro Rosso were invited to the Suzuka meeting – which was the first time that fellow non-FOTA members Ferrari and Sauber have joined talks for some time.
Speaking about the meeting that took place, Horner said: "I don't know what they talked about in the meeting so I couldn't comment on that.
"You have got FOTA that doesn't consist of some teams but does consist of others. I have no idea what the topic of discussion was; they obviously feel that it doesn't apply to Red Bull.
"So I cannot really comment on something that I don't really know about."
McLaren team principal Martin Whitmarsh, who is chairman of FOTA, said that not too much significance should have been given to the fact that Ferrari and Sauber joined the meeting.
"We were just talking about life and times in F1," he said.
"I am not worried about FOTA. It is sensible for teams to try and share some of the issues we have got and try and work together."