Mustafa Suleyman is head of the company’s “applied” division, which looks for practical ways to implement the firm’s research into AI.
In a statement, DeepMind said: “Mustafa’s taking some time out right now after 10 hectic years.”
The company did not say why Mr Suleyman was taking time off but said it was a mutual decision. DeepMind expects him to return to his post later this year.
News of Mr Suleyman’s leave was first reported by Bloomberg, which suggested it was linked to controversies over some of DeepMind’s work in the health industry.
Privacy concerns have previously been raised over some of its use of patient data.
The company’s Streams app has been used at the Royal Free Hospital in London, which processes patient data and could alert doctors if someone is at risk of developing kidney disease, potentially saving half-a-million hours of paperwork and helping to detect illness quicker.
But in 2017, UK data watchdog the Information Commissioner’s Office ruled that the Royal Free NHS Foundation Trust broke data privacy laws when it provided the data of around 1.6 million patients as part of a trial.
It said patients had not been adequately informed that their data would be used as part of the test.
Last year, further concerns were raised after Google announced plans to bring the health division of its DeepMind artificial intelligence company more closely under its control.
Critics said they were concerned that the change could put sensitive data in the tech giant’s hands, despite Google stressing that patient information would remain under the control of the NHS.
Mr Suleyman co-founded DeepMind in 2010 with Demis Hassabis, the firm’s current chief executive.
The company was bought by Alphabet in 2014 for £400 million.