Although the ban remains provisional while the FEI investigates, Dujardin, who has six Olympic medals in total, has said she will “withdraw from all competition while this process takes place”.
“What happened was completely out of character and does not reflect how I train my horses or coach my pupils, however there is no excuse,” she said in statement.
“I am deeply ashamed and should have set a better example in that moment.”
Both the British Equestrian (BEF) and British Dressage (BD) have also imposed a provisional suspension on Dujardin pending the outcome of the FEI investigation.
In a statement the FEI added it “intends to proceed [its investigation] as swiftly as possible”.
“It is our responsibility and crucial that we address any instances of abuse, as equine welfare cannot be compromised,” said FEI president Ingmar De Vos.
“Charlotte [Dujardin] has expressed genuine remorse for her actions, and we recognise and appreciate her willingness to take responsibility.
“Despite the unfortunate timing, we believe this action reaffirms the FEI’s commitment to welfare as the guardians of our equine partners and the integrity of our sport.”
At the last Olympics in Tokyo in 2021, German modern pentathlon coach Kim Raisner was disqualified from the Games for appearing to punch a horse.
That incident sparked a major overhaul of the event with the equestrian element replaced by an obstacle course.
Becky Moody and her horse Jagerbomb are Team GB’s alternate combination for the dressage.
The British Olympic Association (BOA) said it “will be applying to bring in a reserve athlete under the IOC’s Late Athlete Replacement rules”.
It added: “The BOA takes animal welfare extremely seriously, and we believe that everyone has a responsibility for ensuring the wellbeing of horses.”
British Dressage chief executive Jason Brautigam said: “These historic allegations are deeply upsetting for everyone involved in our sport, but we fully support the FEI investigation and will take any appropriate disciplinary action when this process is complete.”
British Equestrian chief executive Jim Eyre said the BEF would “fully comply with any [FEI] requests to fulfil their investigation”.
He added: “As the guardians of equestrian sport, we must uphold the highest standards of equine welfare – the horse’s wellbeing is paramount.”