NEW YORK, N.Y. – If the Church of Scientology was hoping that HBO’s withering documentary on the religion’s practices would pass by with little notice, that turned out to be a miscalculation.

“Going Clear: Scientology and the Prison of Belief” has been seen by more than 5.5 million people since its debut two weeks ago. It is likely to wind up being second only to a 2013 movie on Beyonce as the premium cable network’s most-watched documentary of the past decade, HBO said Monday.

It has been an extraordinary two months for HBO’s film unit. The six-part series on billionaire Robert Durst, “The Jinx,” was a sensation with its climax reaching nearly 5 million viewers. Durst was arrested for murder on the eve of the series’ last episode, in part due to evidence uncovered by the filmmakers.

The Church of Scientology ran a full-page advertisement in The New York Times denouncing the film before it ran, questioning whether “Going Clear” would turn out to be like Rolling Stone magazine’s since-retracted story about an alleged sexual assault at the University of Virginia.

“I didn’t think we expected this kind of noise and this kind of energy, but we’ll take it,” said Sheila Nevins, the veteran chief of HBO’s documentary unit. “I didn’t think it would be this controversial.”

Director Alex Gibney made “Going Clear,” based on the book by Lawrence Wright. Gibney also did “Mea Maxima Culpa: Silence in the House of God,” an investigation into sex abuse in the Catholic Church, for HBO.

Although “Going Clear” details church attempts to respond aggressively to people questioning their practices, Nevins said she was surprised at how church lawyers and officials questioned the film and HBO before it aired.

“I really thought they would be smart to keep their mouths shut and let it go by,” she said.

HBO’s Beyonce film was seen by more than 9 million people, and both parts of a 2006 film on Hurricane Katrina reached more than 6 million viewers, according to the Nielsen company. Since HBO is still airing “Going Clear” regularly and it is available on demand and via stream, HBO said it expects this year’s film to surpass the “When the Levees Broke” film.

Nevins said she’s already worried about what she can do to follow up the current success.

“How do you match Durst going into the bathroom (and discussing the murders he stands accused of)?” she said. “How do you match people taking out a full-page ad in the New York Times and it’s not your obituary?

“The real problem for anxiety-prone people like me is what comes next,” she said.