Agnel was ruled to have come third behind Jeremy Stravius and Jordan Pothain in the final at the French championships, which served as the Olympic trials, after failing to touch the finishing pad correctly.
Only the first two qualified for the Rio Games but Pothain has decided to swim the 400 freestyle instead thereby opening the way for Agnel to compete at the Rio Games.
"It's up to him to decide his programme. He's got a reserved spot on the 200 metres freestyle," FFN technical director Jacques Favre said.
"Jordan Pothain has decided to swim the 400 metres freestyle and not the 200 metres, that's his strategy."
Pothain said last week that he would be ready to pull out of the 200 freestyle to make room for Agnel after TV footage appeared to show that Agnel had touched home in second.
(Reporting by Julien Pretot; Editing by Ken Ferris)
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