“Our hope is that removing an article that is in conflict with both our values and what we aspire to as journalists will demonstrate how seriously we take our error,” according to an editors’ note that went up in place of the story. “We were wrong. We will do better.”

In an earlier note, after the story was revised in response to the barrage of criticism, The Daily Beast’s editor in chief, John Avlon, said editors had removed details that might identify the athletes. He also responded to complaints that Mr. Hines’s original article mocked or shamed the athletes who responded to Mr. Hines’s overtures on Grindr.

“We do not feel he did this in any way,” he said.

Mr. Avlon said that Mr. Hines received more invitations on Grindr than on straight dating apps and that “he never claimed to be anyone he was not, did not offer anything to anyone, and immediately admitted that he was a journalist whenever he was asked who he was.”

But at 9 p.m., the article and the original editor’s note were gone, and replaced with a note describing how the organization took the “unprecedented but necessary step” of removing the entire article.

“The Daily Beast does not do this lightly,” the note said. “Our initial reaction was that the entire removal of the piece was not necessary. We were wrong.”