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The Atlantic on Tuesday issued a simple three-word apology for publishing an advertisement by the Church of Scientology that resembled a normal article from the acclaimed magazine: "We screwed up."

The Web page, published around lunchtime on Monday, was labeled as "sponsor content," but otherwise looked like a sunny blog post about the church's expansion. The page was titled "David Miscavige Leads Scientology to Milestone Year." It was noticed by reporters at other news organizations on Monday evening and was stripped from The Atlantic's site by midnight.

"It shouldn't have taken a wave of constructive criticism — but it has — to alert us that we've made a mistake, possibly several mistakes," The Atlantic said in a statement. "We now realize that as we explored new forms of digital advertising, we failed to update the policies that must govern the decisions we make along the way."

In other words: The Web site published Scientology's ad without considering all the consequences.

The Atlantic is far from the only digital publisher pitching advertisers on what is known as sponsored content. Gawker and BuzzFeed are among the other Web sites that have gained attention for the practice, which places an advertiser's words and visuals (the content) within the frame of the site. The Huffington Post has a whole section front for sponsored content.

But no instance of sponsored content has come under as much criticism as this one. Gawker called the sponsored Web page "bizarre, blatant propaganda for Scientology." Others raised questions about why all the comments on the page were supportive of the church, indicating that critical comments were being deleted. A spokeswoman for The Atlantic said that the comments were moderated by its marketing team, not by the editorial team that moderates comments on normal articles.

At the same time, others defended the arrangement as a smart business move. The church's ad buy comes at a time when it is trying to blunt the impact of a new book about the secretive religion by Lawrence Wright, "Going Clear: Scientology, Hollywood and the Prison of Belief." The book will be published on Thursday.

On the same day, the NBC newsmagazine "Rock Center with Brian Williams" will broadcast an interview with the writer and director Paul Haggis, described by the network as "the most famous Scientologist to leave Scientology and speak out against it."

The Atlantic said on Tuesday that it deleted the Scientology ad "until we figure all of this out," meaning the policies that govern sponsored content.

"It's safe to say that we are thinking a lot more about these policies after running this ad than we did beforehand," the magazine said.

The magazine indicated that it was not backing away from sponsored content altogether, far from it: "We remain committed to and enthusiastic about innovation in digital advertising, but acknowledge — sheepishly — that we got ahead of ourselves." The statement concluded, "We are sorry, and we're working very hard to put things right."

The Atlantic spokeswoman said that the handling of comments on sponsored content is one of the issues it is going to review.