Depp's former wife Amber Heard had accused the actor of domestic violence.
Radcliffe, who grew up onscreen as J K Rowling's boy wizard Harry Potter, said although he is grateful to the team for giving him "a great start in life and an amazing job", he believes Depp's behaviour is being tolerated because he is a renowned name in the showbiz.
"I can see why people are frustrated with the response that they were given from that... I'm not saying anything that anybody hasn't already said - and this is a weird analogy to draw (but) in the NFL, there are lots of players arrested for smoking weed and there is other people's behaviour that goes way beyond that and it's tolerated because they're very famous players," Radcliffe told Entertainment Weekly.
"I suppose the thing I was struck by was, we did have a guy who was reprimanded for weed on the (original Potter) film, essentially, so obviously what Johnny has been accused of is much greater than that," he added.
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The 28-year-old actor's comments come after Rowling shared her response to a fan on social media, who questioned the author's agreement to let Depp be a part of the film.
Rowling added both she and David Yates had considered the possibility of recasting the role for "Fantastic Beasts: The Crimes Of Grindlewald".