In an interview with the magazine, the 16-year-old said that he does not agree with abortion and appeared to make a controversial statement regarding pregnancies that are a result of rape.
However, Rolling Stone has since spoken out to clarify the remarks.
"Due to an editing error, this story originally included an incomplete quote from Justin Bieber," the magazine explained.
"The full quote, his response to whether abortions should be allowed in cases of rape, reads, 'Um. Well, I think that's really sad, but everything happens for a reason. I don't know how that would be a reason. I guess I haven't been in that position, so I wouldn't be able to judge that.'"