The 34-year-old world number three's appearance at Roland Garros had been in doubt after he missed the Madrid Open with back problems and suffered an early defeat at the Italian Open in the build-up to the clay court major.
Federer took to Philippe-Chatrier Court for a short practice session on Wednesday in the hope that he had made a return to full fitness in time for his 68th Grand Slam.
“I regret to announce that I have made the decision not to play in this year’s French Open. I have been making steady progress with my overall fitness, but I am still not 100% and feel I might be taking an unnecessary risk by playing in this event before I am really ready,” said Federer in an announcement posted to his Facebook page. “This decision was not easy to make, but I took it to ensure I could play the remainder of the season and help to extend the rest of my career.
“I remain as motivated and excited as ever and my plan is to achieve the highest level of fitness before returning to the ATP World Tour for the upcoming grass court season.
“I am sorry for my fans in Paris but I very much look forward to returning to Roland Garros in 2017.”
Federer completed his career Grand Slam with victory at Roland Garros in 2009, has been dealing with a series of injuries in 2016, including recovery from knee surgery following the Australian Open and a back injury in recent weeks.
"Roger's knees are feeling better, but he’s not fit enough to compete in best-of-five matches," said Roland Garros tournament director Guy Forget.
Federer owns the Open Era record with 65 straight appearances in Grand Slam main draws. His streak stretches to 69 straight appearances including qualifying and 73 including the juniors. The last major that Federer did not appear at was the 1997 US Open.
Date: 19 May 2016, Source: Roland Garros, ATP, and Reuters