Charlotte Dujardin, Britain's joint-most decorated female Olympian, has been provisionally suspended by equestrian's governing body the FEI.
The dressage star had already pulled out of Paris 2024 after a video emerged which she said showed her "making an error of judgement".
The FEI said it had received footage showing three-time Olympic gold medallist Dujardin "engaging in conduct contrary to the principles of horse welfare - during a training session conducted at Ms Dujardin's private stable".
A lawyer representing the claimant who filed an official complaint against Dujardin to the FEI said in an accompanying letter seen by the BBC "the video shows Ms Dujardin beating a horse excessively with a whip".
They added: "My client is aware that this complaint could have far-reaching consequences for Ms Dujardin, including disciplinary sanctions. My client had to think long and hard about whether to bring this to your attention this way."
Good Morning Britain, the ITV breakfast show, aired footage on Wednesday morning that appeared to show Dujardin hitting a horse with a long equestrian whip.
The footage, which is yet to be verified by the BBC, appeared to show Dujardin repeatedly striking the back of a horse's legs.
Whips are used in all equestrian disciplines and when employed as a training aid should be utilised lightly to communicate with the horse.
"In dressage they use a long whip called a schooling whip to encourage the horse," Madeleine Hill, a former dressage reporter for magazine Horse & Hound, told the Today Programme.
"Generally you can't use the whip too harshly because horses are very sensitive and they'll react badly.
“In dressage I would say it's used as a training aid and quite cautiously."
The FEI said Dujardin confirmed she was the individual in the video which was "filmed several years ago" and "requested to be provisionally suspended pending the outcome of the investigations".
The body initially announced a six-month suspension but later said the ban would "remain in place pending the outcome of the investigation/disciplinary proceedings".
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.
The FEI added it "intends to proceed [with 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 at Paris 2024.
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."
Roly Owers, chief executive of World Horse Welfare, said: "We know that a successful future for horse sport has public trust at the centre of it. The public has to trust that equestrians are caring and are treating their horses with respect, compassion and understanding.
"If that trust is damaged it will damage the sport. This is another massive wake-up call for anyone who thinks this is not important, because it most certainly is."
Dujardin, 39, won team and individual gold medals at the London 2012 Games on Valegro, and the pair went on to win individual gold and team silver four years later in Rio.
On a different horse, Gio, she won two bronzes at the delayed Tokyo 2020 Games.
Dujardin had been set to compete in both the individual dressage and team event alongside Carl Hester and world champion Lottie Fry, on new horse Imhotep.
She needed a medal of any colour to take the outright lead as most-decorated British female Olympian from now-retired cyclist Dame Laura Kenny.
Speaking to BBC Sport last week, Dujardin said it felt "surreal" to be on the cusp of that achievement and doing so would be "one of the most incredible moments".
Dressage is the oldest equestrian discipline, and sees rider and horse perform a series of movements to music across the gaits of walk, trot and canter.
Analysis - Laura Scott, BBC sports news correspondent
This news was shocking when it broke and caught a lot of people off guard within the British Olympic setup. It will undoubtedly rock the team with the Games just about to start.
When I went to visit Dujardin at her yard in Gloucestershire three weeks ago, she was confident about making history in Paris and told me she wanted to make her young daughter proud. She was considered a gold medal contender both individually and with the team.
Now she won't be at the Games at all. But beyond the impact on Team GB's medal hopes, this story could have major ramifications for the general acceptance of equestrian sport in society. She is one of the faces of British sport and animal welfare is a subject that draws intense scrutiny.
With only three days before the opening ceremony, the timing of this couldn't be worse, and the consequences could be huge.