In a statement posted online, Shapiro, who runs the conservative Daily Wire, said that the video was posted on his site on Monday while he was on vacation and unable to review it before publication.
"I was uncomfortable with the video, but in the interests of giving my employees the benefit of the doubt — and in the interests of defending satire more broadly — I decided to leave the video up," he said.
He then said that decision was a mistake.
My statement on the Columbus Day video that went up on Daily Wire's Twitter and Facebook yesterday. It has now been justifiably removed. pic.twitter.com/ja6h8cW2af— Ben Shapiro (@benshapiro) October 10, 2017
The animated video portrayed indigenous people in the Americas as cannibals and savages. Columbus's ship then makes landfall, and the explorer is shown teaching them how to farm, raise cattle and construct buildings.
The video then goes on to depict the construction of modern cities, as well as the development of cars, airplanes and rockets.
It ends with a side-by-side comparing Native American "achievements" — "dreamcatchers, tomahawks and cannibalism" — and post-Columbus contributions, which it lists as written language, iPhones and women's suffrage, among other items.
"That was a mistake, and I apologize fully for it," Shapiro continued, noting that the video has since been removed from the site.
The apology marks an about-face for Shapiro, who initially defended the video in the face of criticism. In a statement to CNN on Monday, Shapiro said that "everybody needs to calm down" about the video.
"Conservatives are allowed to make satire, too," Shapiro said in his initial statement defending the video.