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.”