Dujardin had been set to compete in both the individual dressage and team event on horse Imhotep at the Olympics.
The three-time Olympic gold medallist said she was “deeply ashamed” and 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.
She has also had her UK Sport funding suspended pending the investigation, while she was dropped as an ambassador for horse welfare charity Brooke.
A group of leading dressage riders, with signatories including her long-time Team GB colleague Carl Hester, have also condemned Dujardin’s actions.
McEwen, 33, added: “We are 110% behind horse welfare. I definitely don’t condone at all Charlotte’s behaviour, but she has put her hands up to it, owned it and it’s not for me to say, it’s for the course, the process and the people to decide what punishment she should be getting for her actions.
“She is a human being at the end of it, so we have to respect her rights as well.
“It was a shock, but we have come here to do our job as an eventing team, so we have our focus and with eventing, you don’t really get too much time on your hands.
“We’ve seen the news, we’ve read it, it’s deeply sad for our sport, but at the same time I don’t believe our sport is like that and we move on.”