Sources: Chris Cox and Chris Daniels left in part over conflicts with Zuckerberg's plan to integrate Facebook's services into a single privacy-focused platform (Mike Isaac/New York Times)

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SAN FRANCISCO — Two of Facebook’s top executives — one regarded as the company’s No. 3, and the other the head of its WhatsApp messaging service — are leaving after disagreements with Mark Zuckerberg, the chief executive, over the social network’s future direction.

The differences stemmed from Mr. Zuckerberg’s asserting control over his company and its apps — Instagram, WhatsApp and Facebook Messenger — by rolling out a plan to integrate the services into a single privacy-focused platform, according to six people involved in the situation.

The change is a substantial shift for Facebook, which has traditionally encouraged people to publicly share posts, videos and photos. Executives at Facebook who had run the various services were concerned that knitting together the apps would take a toll on the popularity and growth of their individual products, said the people, who were not authorized to speak publicly. And with Mr. Zuckerberg exerting more control, the executives were also fearful of losing autonomy and power, they said.

Chris Cox, Facebook’s chief product officer and a member of Mr. Zuckerberg’s inner circle, is one of the two executives leaving. He alluded to the disagreements on Thursday in a public post about his departure. “As Mark has outlined, we are turning a new page in our product direction,” wrote Mr. Cox, 36. “This will be a big project and we will need leaders who are excited to see the new direction through.”

The other executive who is exiting is Chris Daniels, 43, who runs WhatsApp. Neither one responded to requests for comment.

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Chris Daniels, the head of WhatsApp, is also leaving Facebook.CreditGuillermo Legaria/Agence France-Presse — Getty Images

Facebook is undergoing a tricky transition as it tries to recover from two years of scandals over data privacy and disinformation. Those issues have buffeted the Silicon Valley giant, causing internal turmoil as its leaders have tried to find a way to adjust. Mr. Zuckerberg has made several attempts to rid Facebook of toxic content, false news and other problems, with limited success.

Now, Mr. Zuckerberg is barreling ahead with his shift to focus Facebook on private messaging and away from public broadcasting, even if it means shedding some of his top lieutenants.

Mr. Cox has worked with Mr. Zuckerberg for 13 years and joined Facebook as one of its first 15 software engineers. Mr. Cox also was instrumental in building the News Feed, the stream of posts that people see when they log into the service, and which more recently has been under scrutiny for being a hive of misinformation. Among some in Silicon Valley, he had been mentioned as a possible successor to Mr. Zuckerberg.

“Embarking on this new vision represents the start of a new chapter for us,” Mr. Zuckerberg said in a note to staff on Thursday. “While it is sad to lose such great people, this also creates opportunities for more great leaders who are energized about the path ahead to take on new and bigger roles.”

The departures add to the executive turnover at Facebook, which for years had been stable in its top ranks. Mr. Zuckerberg kept close many key executives, including his chief operating officer, Sheryl Sandberg, as well as Mr. Cox and others.

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But that bench has undergone numerous changes more recently as Facebook has grappled with its lapses and tried to reorient itself. Last year, Kevin Systrom and Mike Krieger, the co-founders of Instagram, left the company after clashing with Mr. Zuckerberg over the future of the photo-sharing network. Jan Koum and Brian Acton, the co-founders of WhatsApp, also left after similar disagreements with Mr. Zuckerberg. Other executives, including Facebook’s head of communications and policy and its security chief, have also departed.

Ben Horowitz, a venture capitalist at Andreessen Horowitz, said on Twitter that Mr. Zuckerberg’s new direction for Facebook was controversial because it was such a cultural departure for what had been an open and public social network. But he said Mr. Zuckerberg appeared committed to privacy by plowing ahead with the changes even “in the face of extremely strong dissent.”

“So much so, that he is willing to lose outstanding executives who disagree with this direction,” Mr. Horowitz said. (Mr. Horowitz is a partner at Andreessen Horowitz with Marc Andreessen, a venture capitalist who sits on Facebook’s board.)

Inside Facebook, frustration over Mr. Zuckerberg’s planned changes have been mounting for months, said the people involved the situation. Combining Instagram, WhatsApp and Messenger will be a companywide effort that will take years of infrastructure work and deep changes to some of its products, they said.

Mr. Daniels, who previously ran Facebook’s business development team and had other roles, was appointed head of WhatsApp last May. He became upset at some of the choices that were being made to connect the apps, said people familiar with his thinking. He was also concerned that Mr. Zuckerberg’s plan would harm the success of WhatsApp, which is particularly popular outside the United States.

Because of those changes, Mr. Daniels handed in his resignation months ago, said two of the people, though the decision did not become public until Thursday.

Mr. Cox has also been frustrated with Mr. Zuckerberg’s decisions in recent months, some of the people said. Less than a year ago, Mr. Cox shifted into one of the most powerful positions at Facebook as chief product officer, responsible for overseeing Instagram, WhatsApp, Messenger and Facebook itself.

Almost immediately, Mr. Cox ran into difficulties, the people said. Employees said he disagreed with some of Mr. Zuckerberg’s product ideas and changes, including the “unified messaging” project intended to connect the apps.

But Mr. Zuckerberg had already made his decision. Mr. Cox informed Facebook of his decision to leave on Monday, according to a company filing.

“For over a decade, I’ve been sharing the same message that Mark and I have always believed: Social media’s history is not yet written, and its effects are not neutral,” Mr. Cox said in his post. “As its builders we must endeavor to understand its impact — all the good, and all the bad — and take up the daily work of bending it towards the positive, and towards the good.”

Mr. Zuckerberg has promoted others to take the place of those who have left. Adam Mosseri, a longtime Facebook employee, was promoted to head of Instagram last year. On Thursday, Mr. Zuckerberg said Will Cathcart, another Facebook employee, would run WhatsApp, and Fidji Simo would lead Facebook’s main app.