Koum and his co-founder Brian Acton developed WhatsApp with a focus on user privacy and a disdain for advertising.
However, according to the Washington Post, Koum is leaving over disagreements with Facebook executives interested in weakening WhatsApp's encryption in order to more easily monetize the messaging platform. In a post on Facebook, he said he was "taking some time off to do things I enjoy outside of technology".
Facebook chief executive Mark Zuckerberg replied to Koum's post and said he respected his decision. Facebook's poor privacy protections were exposed last month during the fallout of the Cambridge Analytica scandal, which centered on a quiz app that sucked up user data, and their friends' data.
"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 centralised systems and put it back in people's hands. And I'll still be cheering WhatsApp on - just from the outside".
Acton left WhatsApp late previous year and joined in the growing backlash against Facebook, endorsing a campaign that encouraged users to delete their profiles from the social network.
The first comment to appear below Koum's Facebook post is a carefully worded statement from Facebook's CEO Mark Zuckerberg.More news: 'Solo: A Star Wars Story' Gets A New Dolby Cinema Poster
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On his social media post, Koum announced his exit from the company, however, there is no any particular reason claimed by him.
WhatsApp, a pun on the phrase "What's up?" grew in popularity in part because its messages are stored on users' smartphones and not on the company's servers, making the service more private and hard to hack.
Koum did not reveal when exactly he would depart the company.
Koum also signaled years ago that he would take a stand against Facebook if the company's push to increase its profits demanded radical changes in the way WhatsApp operates.
Facebook bought WhatsApp in 2014, and back then, Koum wrote that the deal wouldn't have happened if WhatsApp "had to compromise on the core principles that will always define our company, our vision and our product".
Messrs. Koum and Acton had clauses in their contracts with Facebook that allowed an acceleration of their contracts if Facebook added advertising to the app. Mr. Koum's contract with Facebook wasn't supposed to end until November, the person familiar with the matter said.