In the new film, Hathaway stars as the Grand High Witch, who is missing fingers on each hand.
Many people have spoken out against the character, with British Paralympic swimmer Amy Marren saying that those with limb differences are 'represented as something scary'.
Hathaway has now said she is sorry for 'pain caused' by the role, having promised to 'do better' in the future in a statement on Instagram.
Sharing a video from a charity called Lucky Fin Project, she wrote: "I have recently learned that many people with limb differences, especially children, are in pain because of the portrayal of the Grand High Witch in The Witches.
"Let me begin by saying I do my best to be sensitive to the feelings and experiences of others not out of some scrambling PC fear, but because not hurting others seems like a basic level of decency we should all be striving for.
"As someone who really believes in inclusivity and really, really detests cruelty, I owe you all an apology for the pain caused.
"I am sorry. I did not connect limb difference with the GHW when the look of the character was brought to me; if I had, I assure you this never would have happened.
"I particularly want to say I'm sorry to kids with limb differences: now that I know better I promise I'll do better.
"And I owe a special apology to everyone who loves you as fiercely as I love my own kids: I'm sorry I let your family down."
Warner Bros has also apologised, with a statement provided to US Weekly saying it was 'deeply saddened to learn that our depiction of the fictional characters in The Witches could upset people with disabilities', adding that it 'regretted any offence caused' by the film.
"In adapting the original story, we worked with designers and artists to come up with a new interpretation of the cat-like claws that are described in the book," a spokesperson said in the statement.
"It was never the intention for viewers to feel that the fantastical, non-human creatures were meant to represent them.
"This film is about the power of kindness and friendship. It is our hope that families and children can enjoy the film and embrace this empowering, love-filled theme."
Featured Image Credit: Warner Bros