The 21-year-old had marked himself as a contender for the French Open title after lifting the Barcelona crown and making the Madrid semi-finals, though he retired from Rome this month while trailing Andrea Pellegrino in the second round.
"In Rome, I felt a little bit like around the hip, you know, pain. It was bothering me a lot. I didn't want to take any risk," Fils told reporters. He said the exams he did later looked "pretty fine", but the pain persisted.
"I wasn't able to practice for the last two weeks. Actually, the practice today was my first points since two weeks in Rome," Fils said.
"I'll not be fit 100% to play the tournament, and I'll not take any risk like I did last year. I don't want to be stupid."
Fils was due to face Stan Wawrinka in the opening round.
The Frenchman's pullout follows a pattern of injuries stalling his progress. Last year, he pulled out of Roland Garros after the second round with a stress fracture in his lower back.
That issue all but wiped out the rest of Fils' season last year, with his brief return in Toronto in August proving to be premature and forcing another long period of rehabilitation.
Since his return in February, Fils made deep runs at Doha, Indian Wells and Miami before going all the way in Barcelona, where he downed Andrey Rublev in the final to win his first title since his comeback.
Yannick Noah is the only Frenchman to win a Grand Slam in the professional era, claiming his home major in 1983.
The French Open begins on Sunday.