The video showed Logan Paul and friends at the Aokigahara forest at the base of Mount Fuji, known to be a frequent site of suicides.
Going in to film the "haunted" forest, they come across a man's body and are shocked but also make jokes.
Online comments have called the video "disrespectful" and "disgusting".
The video was uploaded on Sunday and had millions of views on YouTube before it was taken down.
Logan Paul, who has more than 15 million subscribers on YouTube, posted an apology on Twitter, saying he had been "misguided by shock and awe".