Had he finished in the top two, Agnel would have retained a chance of being drafted for the Olympics, but his third place means he has no prospect.
"For me I was second, it was quite clear," said Agnel. "Everyone I have met said I had evidently touched second, by quite a distance, and that there was no doubt. I believe their word."
Agnel's coach later told AFP the swimmer would appeal to the French Olympic Committee while French Swimming Federation (FFN) president Francis Luyce accepted responsibility for the fact video evidence was not used.
"The rules stipulate that we cannot take into consideration the images, that we have not seen," he said.
The race continues an ongoing controversy in French swimming after the FFN released Olympic qualifying standards much higher than the official times requested by international governing body FINA.
All of the top four in the race on Wednesday met the standards set by FINA, but all fell below the FFN time, meaning that Stravius and Pothain's Rio hopes remain in the balance.
Former backstroke specialist Stravius' time was the fourth best in the world this season, while even Agnel's third-placed effort puts him in the top 10.
Agnel could yet still go to Rio, however, as part of the French relay teams.
- news.com.au