Dujardin had been set to compete in both the individual dressage and team event alongside Hester and world champion Lottie Fry, on horse Imhotep.
The three-time Olympic gold medallist said she was “deeply ashamed” and that her actions were “completely out of character”.
Both British Equestrian (BEF) and British Dressage (BD) have imposed a provisional suspension on Dujardin pending the outcome of the FEI investigation.
On Wednesday, Dujardin had her UK Sport funding suspended pending the investigation, while she has also been dropped as an ambassador for horse welfare charity Brooke.
Two of her sponsors, equestrian insurance company KBIS and Danish equestrian equipment company Equine LTS, have terminated their deals with her.
Meanwhile, Team GB chef de mission Mark England said Dujardin had been offered support from the British Elite Athletes Association.
“She’s going through a difficult time,” England told Sport. “What’s important is, as a valued member of Team GB and as an Olympic champion, that we do wrap some care around her.
“It is a very difficult error of judgement by her standards and by her own admission. We wish her well but we don’t condone what has happened.
“Animal welfare and the welfare of everybody in Team GB is really important.”
