The sponsored post, which went live Monday at 9:25 a.m. PT, touted 2012 as "milestone year" for the secretive church, which has been steeped in controversy throughout the years.
It was taken down about 8:30 p.m. and replaced by a message saying the magazine had "temporarily suspended this advertising campaign pending a review of our policies that govern sponsor content and subsequent comment threads."
"We screwed up," Natalie Raabe, an Atlantic spokeswoman told TheWrap after the firestorm of criticism and mockery the advertisement generated on the web. "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 issued the following statement:
We screwed up. 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. 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. It's safe to say that we are thinking a lot more about these policies after running this ad than we did beforehand. In the meantime, we have decided to withdraw the ad until we figure all of this out. We remain committed to and enthusiastic about innovation in digital advertising, but acknowledge - sheepishly - that we got ahead of ourselves. We are sorry, and we're working very hard to put things right.
The timing of the ad was no surprise. New Yorker writer Lawrence Wright's book-length expos on Scientology - based on his 2011 profile of former Scientologist Paul Haggis - is due out Thursday.
Sponsored content, otherwise known as native ads or advertorials, have become a popular source of revenue for online publications, including Forbes and Business Insider.
But, normally, advertisers do not want comment threads under their paid-for content, and while this has never been a problem for previous Atlantic clients, the heated feelings surrounding Scientology erupted in the comment section below the article.
The Atlantic's marketing team was moderating the comments - about 20 in all before the post was pulled - as they were posted, Raabe said.
"In this case, where a mistake was made, where we are taking a hard look at these things, is there were comments allowed on this post," an Atlantic official with knowledge of the situation told TheWrap. "For a subject like this where people very strong feelings, we realized there's not a clear policy in place for things like commenting."
The Church of Scientology told TheWrap no one was available to speak on the controversy, and its media relations team did not immediately respond to an email requesting comment.