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".
He later uploaded a video apology, and said: "I should have never posted the video. I should have put the cameras down and stopped recording what we were going through."
"I'm ashamed of myself," he added. "I'm disappointed in myself."
Japan has one of the highest rates of suicide in the developed world.
Aokigahara has a tragic reputation in Japan and internationally as a destination for people who want to kill themselves.
Data on the number of suicides there each year is not made public, to avoid publicising the site. Signs are posted in the forest urging people to seek medical help rather than take their own lives.
The 15-minute video is part of a series of posts from Japan where the US vlogger is on a trip with friends.
They go on a visit to the forest intending to focus on the "haunted" aspect of it, he says in the video.
After walking a short distance into the forest, the group come across a body.
The group is filmed approaching the body, which is shown in several close-ups where only the face is blurred out.
A member of the group is heard off camera saying he "doesn't feel good". Paul then asks him: "What, you never stand next to a dead guy?" He then laughs.
The identity of the deceased man is not known.
By Monday, Logan Paul's name was trending globally on Twitter. Though some people said he had helped raise awareness, the comments were overwhelmingly negative.
Online comments have accused him of acting inappropriately and being disrespectful. Some have called for his entire channel to be removed from YouTube.
Some supporters insisted he should be forgiven for what they said was a mistake, with one tweeting: "You still are the best out there and always will be" with the hashtag #Logan_you_are_forgiven.
In an apology posted on his Twitter page, Paul, of Westlake, Ohio, said: "I'm surrounded by good people and believe I make good decisions, but I'm still a human being. I can be wrong."
He goes on to say he wanted to "make a positive ripple on the internet, not cause a monsoon of negativity", by raising awareness of suicide and suicide prevention.
Paul says in the video that he is not making money off the content. YouTube, which pays content providers for videos that garner above a certain number of hits, did not immediately respond to the BBC's request for comment.