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Federer struggled with injury at this year's Australian Open in Melbourne, where he lost in the semi-finals to eventual champion Novak Djokovic, and subsequently underwent surgery on the knee in February.
"A few weeks ago, having experienced a setback during my initial rehabilitation, I had to have an additional quick arthroscopic procedure on my right knee," the 38-year-old said in a Twitter post.
With professional tennis shut down due to the COVID-19 pandemic it remains to be seen how many tournaments Federer will actually miss.
The Swiss also had knee surgery to repair a torn meniscus in 2016 and missed the second half of that season.
When he returned to the tour for the 2017 season it looked like he had never been away, winning the Australian Open to end a near five-year Grand Slam title drought and adding the Wimbledon title later that year.
The last of Federer's record 20 Grand Slam singles titles came at the 2018 Australian Open. The closest he has come since was at Wimbledon last year when he lost in the final.
"Now, much like I did leading up to the 2017 season, I plan to take the necessary time to be 100% ready to play at my highest level," he said.
"I will be missing my fans and the tour dearly but, I will look forward to see everyone back on tour at the start of the 2021 season."