Depp was accused of domestic abuse by ex-wife Amber Heard in 2016 after 16 months of marriage. He has always denied all allegations of abuse.
Depp and Heard later released a joint statement after reaching a settlement in which they acknowledged their relationship was "volatile".
It said: "Neither party has made false accusations for financial gain. There was never any intent of physical or emotional harm."
But many fans have said they are unhappy with his involvement in the movie in light of the allegations, which surfaced as his cameo in the first movie was being filmed.
In a statement, JK Rowling addressed the criticism, saying Depp and Heard’s privacy “must be respected”.
“When Johnny Depp was cast as Grindelwald, I thought he’d be wonderful in the role. However, around the time of filming his cameo in the first movie, stories had appeared in the press that deeply concerned me and everyone most closely involved in the franchise.”
She said that fans had “legitimate questions”over the casting, and she understood “why some have been confused and angry”.
The author added: "The filmmakers and I are not only comfortable sticking with our original casting, but genuinely happy to have Johnny playing a major character in the movies."
She concluded: “I accept that there will be those who are not satisfied with our choice of actor in the title role. However, conscience isn’t governable by committee.
“Within the fictional world and outside it, we all have to do what we believe to be the right thing.”
But some fans weren't satisfied with her response.
You can say what you want but as long as crusty Johnny Depp is in it I'm out— King Giroud (@YoungeArsenal) December 7, 2017
dear J.K,— lohseok; 承 RT NO FIXADO (@allformyhobi) December 7, 2017
I love you, you're responsible for the person I am today but I'm sorry, as long as Johnny Depp is in the cast I'm not going to see the movie. That's it!
Fantastic Beasts: The Crimes Of Grindelwald is set for release in November 2018.