The 20-time Grand Slam champion had arthroscopic surgery on his right knee - which had been "bothering him for a little while" - in Switzerland.
Federer, who won his only Roland Garros title in 2009, said doctors were "very confident of a full recovery".
"After the procedure, the doctors confirmed it was the right thing to have done," the 38-year-old said.
In addition to the French Open, which takes place from 24 May-7 June, Federer will also miss the tournaments in Dubai, Indian Wells, Bogota and Miami.
Federer reached the semi-finals last year in his first appearance on the Paris clay since 2015.
"See you on the grass!" added the eight-time Wimbledon champion, who was knocked out of last month's Australian Open in the semi-finals by Novak Djokovic.
Spain's Rafael Nadal will be looking to win his 13th French Open title, which would see him draw level with Federer on 20 Grand Slams.