Klein has been replaced by Ken Jautz, who currently runs HLN, said Jim Walton, CNN Worldwide President. CNN is also seeking another executive who will serve as executive vice president and managing editor of CNN Worldwide.
CNN slipped behind MSNBC into third place this year in its prime-time ratings, where Fox News Channel remains a dominant number one. Cable news viewers have increasingly become interested in hearing news filtered through strong, partisan viewpoints and CNN has resisted that approach for fear it would hurt its brand as an impartial news source.
The image of CNN as hurting particularly frustrates Walton, who noted that prime-time advertising accounts for only 10 percent of the company's revenue. CNN has been profitable for seven consecutive years during a disastrous time for the news industry, he said.
"CNN is not broken," he said. "While we're not satisfied with the ratings at CNN prime time and they clearly need to get better, CNN as an organization and a business is thriving."
Klein has held his job for six years, overseeing more aggressive news coverage and the development of Anderson Cooper and Sanjay Gupta as major personalities. The former CBS News executive said he's confident CNN is better today than when he arrived in December 2004.
"I'm disappointed, but these things happen in the media business," Klein said, "and they happened to me this time."
The timing was odd given that Klein's reboot of two-thirds of CNN's prime-time schedule was to begin on Oct. 4. That's when an 8 p.m. show hosted by former New York Gov. Eliot Spitzer and newspaper columnist Kathleen Parker is to debut.
In December, Larry King will leave CNN's prime-time lineup after a quarter-century, to be replaced in January by British tabloid veteran and "America's Got Talent" judge Piers Morgan.
"I'm just disappointed that I didn't get a chance to work more closely or longer with Eliot and Kathleen and Piers," Klein said. "I was really looking forward to getting these shows up and running and fully prepared for being held accountable for their quality and their ratings and their profits. The surprise to me was that I never got a chance to do this."
Walton said he made the move now to avoid disruptions to these programs after they started, and so that the executive change not be interpreted as any dissatisfaction with them.
Klein received praise from a competitor on Friday.
"Jon is a respected journalist and an expert in the digital realm," said Roger Ailes, Fox News chairman and CEO. "We've enjoyed competing with CNN during his tenure and I'm confident he'll be an asset to any news organization he joins in the future. I look forward to continuing our personal dialogue."
Prime-time viewership is down at all the cable news networks this year, but the drop is largest at CNN. Its weekday average of 640,000 viewers is down 36 percent from 2009. Fox is averaging 2.43 million viewers, down 5 percent. MSNBC is down 11 percent to 846,000 viewers, according to the Nielsen Co.
HLN, formerly CNN Headline News, is averaging 554,000 viewers in prime-time. Jautz was in charge of a transformation of that network, once known for its continuous "wheel" of half-hour newscasts. Its shift to a prime-time opinionated lineup began with current Fox personality Glenn Beck, and now features Nancy Grace, Jane Velez-Mitchell and Joy Behar.
Jautz is a "smart, talented executive with the right personality and skill set to restore CNN's position in the cable news space," said Princell Hair, a former CNN executive now senior vice president for news operations at Comcast Sports.
Frank Sesno, a former CNN Washington bureau chief and now a professor at George Washington University, said Klein's departure isn't surprising but the timing was odd.
"CNN is an incredible franchise with what should be an incredible product brand and it's still trying to find itself," he said. "Jon Klein is just the latest. If you telescope the whole thing, CNN has been going through this for 10 years. The real question is what is Ken Jautz going to do."
Walton said that CNN will not move in the same direction as Fox and MSNBC.
"It's critical for the entire business of CNN Worldwide that we remain nonpartisan," he said. Walton appointed Scott Safon, CNN's chief marketing officer, to become HLN's chief executive. Despite Safon's non-news background, his role in Walton's inner circle exposed him to all facets of the business, Walton said.