The rumours began to circulate in July after Baron Cohen left the project because of creative differences with the surviving Queen members.
Radcliffe told Empire magazine: "There’s no truth to it at all. It’s one of those very, very funny things: it came out of a story in the Daily Star and then you see newspapers like The Guardian using The Star as their source, and it grows and grows until it's 'Daniel Radcliffe playing Freddie Mercury!', which I was never going to do."
He said he agreed with those who claimed he would not be suited to the role.
"Everyone on the internet who I presume is saying I'm totally wrong for the part is correct," he said. "I am completely wrong for the part!"
Radcliffe added: "This is the kind of thing that happens to me and it happens to Emma [Watson] with multiple Fifty Shades of Grey things. When somebody has column inches to fill, they just sub in one of our names."
Speaking earlier this month, he said: "Needless to say I wouldn't be involved, and I guess none of the others will be, but I know nothing about it."
The new film, which will start 70 years before Harry Potter’s adventures in The Philosopher’s Stone, will feature Newt Scamander, the fictional author of the textbook.