The controversies have prompted disagreements among top Facebook executives about how to deal with those issues. In March, The New York Times reported that Alex Stamos, Facebook’s chief information security officer, intended to leave the company after an internal dispute over how to handle the threat of Russian influence efforts. Facebook has also reshuffled the top ranks of its Washington office, where lobbying and policy matters are handled.
Facebook declined to comment beyond Mr. Koum’s post. Mr. Koum’s decision was earlier reported by The Washington Post.
Facebook’s business depends on getting people to spend time on its sites and allowing advertisers to target users based on their interests. WhatsApp has had no advertising on its service, but in recent years it has been sharing more information about its users with Facebook.
In March, Brian Acton, who co-founded WhatsApp with Mr. Koum and who has since left the company, wrote on Twitter that it was time to delete Facebook after the Cambridge Analytica revelations.
Mr. Koum and Mr. Acton, who met at Yahoo while doing a security audit for the company, founded WhatsApp in 2009. Originally, the service was a way for people to tell friends and family whether they were available to text and talk. But it soon morphed into a general and free way of sending messages without the help of the services run by cellular network operators like Verizon and AT&T.
WhatsApp became enormously popular in countries where messaging services were expensive or where social networks like Facebook had not taken hold. By February 2014, WhatsApp had about 450 million users and 50 employees. Facebook’s acquisition of the company turned many WhatsApp employees into millionaires.
In the spring of 2016, Mr. Koum and WhatsApp revealed that it was adding end-to-end encryption to every form of communication on the company’s service, which was by then used by more than 1 billion people across the globe. That meant that even company employees could not see messages, phone calls, photos or videos sent across the WhatsApp network, and the company had no way of complying with any court order demanding access to those communications.
Though Mr. Koum joined the board of Facebook after his company was acquired, WhatsApp continued to operate independently in many ways. Its staff remained small, and they worked from their own office in Mountain View, Calif., away from Facebook’s headquarters in Menlo Park, Calif. The Mountain View building carried the names of neither Facebook nor WhatsApp on the outside.
While WhatsApp does not carry advertising, the company has worked over the past two years to create ways for businesses to communicate with customers via its service.
In 2016, WhatsApp said it would start disclosing the phone numbers and analytics data of its users to Facebook. A year later, the European Commission fined Facebook 110 million euros, or about $122 million, for misleading the commission during its acquisition of WhatsApp, saying that Facebook incorrectly claimed that it was impossible to combine user data collected by the two companies.
Last November, Mr. Acton left WhatsApp and later became the executive chairman of the Signal Foundation, the nonprofit that has run the encrypted communication app Signal.
By then, Mr. Koum had also shared his unease over Facebook’s data and privacy policies with others, according to the company executive who has spoken with Mr. Koum. While Mr. Koum personally got along with Mark Zuckerberg, Facebook’s chief executive, he felt the company’s board simply paid lip service to privacy and security concerns he raised, according to the executive.
In particular, the executive said, Mr. Koum was tired from fighting back against pressure from the board throughout 2017 to allow advertisements on WhatsApp.
Facebook did not intend to announce Mr. Koum’s departure until later this week, the person added. Facebook will hold its annual developer conference in San Jose, Calif., on Tuesday and Wednesday and it wanted to first get past the event. But The Post’s report foiled those plans, the executive said.
“Jan and Brian’s departures mean that Facebook, WhatsApp and Instagram are all controlled even more tightly by a single person — Mark Zuckerberg,” said Sandy Parakilas, a former Facebook manager who is now an adviser at The Center for Humane Technology. “This centralized control is bad for the users of all of these products.”
Mr. Koum’s departure was a blow to those at WhatsApp, according to one engineer at the messaging service, who asked not to be identified for fear of retaliation. There had been a certain level of pride within WhatsApp’s team over the dedication to privacy and the departure of their co-founder had left many wondering whether Facebook would now open WhatsApp to tracking user data and, eventually, to ads on its service.
Mr. Zuckerberg said in a comment on Mr. Koum’s Facebook post that he would miss working with Mr. Koum.
“I’m grateful for everything you’ve done to help connect the world, and for everything you’ve taught me, including about encryption and its ability to take power from centralized systems and put it back in people’s hands,” Mr. Zuckerberg wrote. “Those values will always be at the heart of WhatsApp.”