Facebook's ranking as the best place to work in the United States takes a dive after 2018's scandals. Instead, it was using the certification - which should only be used to create employee apps - to quietly make a consumer-accessible app, which circumvents Apple's standard review process.
Google appears confident it would quickly regain its access.
Update 31/01/2019 6:04pm ET: According to a tweet from New York Times reporter Mike Isaac, Apple has restored Facebook's enterprise developer certificate. Its developers work on code on Facebook's internal systems. The company noted that the issue had no impact on its consumer services. Many Google employees use Android devices, so Apple's move was likely tougher on Facebook.
What just happened? If this week has shown us anything, it's proved how much power Apple holds within the tech industry.
Apple didn't return a request for comment on the restoration of the Enterprise Certificate. Apple may have to revamp its enterprise developer program so that this secret practice is not repeated.
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While both research programs let the internet giants track activity, Facebook's was more invasive because the company could see much more traffic from users' phones. Onavo's findings helped Facebook executives predict which apps were rising and trending across App Stores.
As it did to Facebook earlier this week, Apple has now revoked a certificate that allows Google to run pre-production and internal iOS apps.
Facebook also said that fewer than five percent of users who participated in the market research program were teens.
Facebook COO Sheryl Sandberg also defended the app recently in an interview with CNBC stating: "The important thing is that the people involved in that research project knew they were involved and consented".
The reference to encrypted data is meant to differentiate Google's app from Facebook Research, which Facebook said could collect data in some instances "even where the app uses encryption, or from within secure browser sessions".
Moreover, Apple is well-known to have been an outspoken advocate of the importance of privacy rules, with CEO Tim Cook praised EU rules during an appearance at the European Parliament a year ago.
In an earlier statement, Facebook had been keen to shut down reports that the company had been accused of "spying" on teenagers through the use of the application in question.