The Times says Stamos had been a forceful advocate for investigating and revealing the company's role in Russian meddling on the platform "to the consternation" of executives such as COO Sheryl Sandberg. "Alex Stamos continues to be the Chief Security Officer (CSO) at Facebook", the statement said.
However, while both Facebook and Stamos said he is now still with the company, neither denied he would be leaving in the near future.
Stamos' departure was reportedly decided on a year ago, but the company made a decision to keep him on until August to help transition his duties to others - and so that it wouldn't look quite as bad for Facebook amid continued discoveries about Russia's abuse of the platform during the 2016 USA election.
Lawmakers have criticized Facebook and other tech giants for allegedly not doing enough to fight Russian influence in the 2016 election.
"Despite the rumors, I'm still fully engaged with my work at Facebook", he tweeted. "I'm now spending more time exploring emerging security risks and working on election security", Stamos wrote. It's true that my role did change.
A Facebook spokeswoman echoed Stamos' sentiment in a statement. The company persuaded him to stay on through August because - in case you haven't noticed - Facebook has been in the middle of the biggest crisis of its life since the full extent of the disinformation campaign became clear past year. "He is a valued member of the team and we are grateful for all he does each and every day".
The Times report also follows Facebook's announcement last week that it had suspended Cambridge Analytica over evidence that it used data from 50 million user profiles to craft messages on the social network designed at influencing elections.
In recent months, Stamos has been among the Facebook executives willing to talk about the company and its ongoing problems on Twitter. Facebook has promised an investigation and Cambridge has denied any wrongdoing. Facebook suspended Cambridge's access late Friday.