Apple has removed Facebook's Onavo security app from the App Store because it does not comply with its privacy rules.

"We work hard to protect user privacy and data security throughout the Apple ecosystem," an Apple spokesperson said in an email to CNBC on Wednesday. "With the latest update to our guidelines, we made it explicitly clear that apps should not collect information about which other apps are installed on a user's device for the purposes of analytics or advertising/marketing and must make it clear what user data will be collected and how it will be used."

According to a Wall Street Journal story on Wednesday, citing a person familiar with the matter, Apple officials told Facebook last week that Onavo violated the company's rules on data collection by developers, and suggested last Thursday that Facebook voluntarily remove the app.

Facebook acquired Israel-based Onavo in 2013, snapping up the free security app that lets users access a virtual private network, or VPN, to browse the web and download apps with a greater degree of privacy. Facebook in the past has offered that service to users without clearly disclosing that it owns the app, and has collected data about what other types of apps those customers use.