"I won't be playing at Indian Wells or in Miami and the goal going forward is to recover in time for the clay-court season".
Rafael Nadal, meanwhile, was forced to pull out of this week's tournament in Acapulco, with the hip muscle problem he suffered in Australia still bothering him, and could yet miss more events.
It marked the sixth tournament in a row that Nadal has pulled out of or retired from - Basel, Paris, the London ATP Tour Finals, Brisbane, Australian Open and Acapulco.
"Unfortunately, the injury I suffered in Acapulco before starting the tournament is in the same area as the one suffered in Melbourne", he posted on Facebook today.
It means Nadal would have been "defending" 690 points while Federer, who won both tournaments, could lose as many as 2000. It was very painful to retire from Acapulco and it is very hard as well to not play in the USA.
French duo Richard Gasquet and Jo-Wilfried Tsonga have also been ruled out of Indian Wells due to knee injuries with Jeremy Chardy, Laslo Djere and Lukas Lacko replacing the trio in the main draw. "They are both fantastic events but coming back from a big surgery is complicated and, after having played a few tournaments, I have discussed with my team that it is best for me to build on the progress and go back to practice".
"Doctors have told me that it is impossible to play, regardless of whether it hurts", Nadal said on Saturday.
The BNP Paribas Open at Indian Wells begins next week while the Miami Open follows two weeks later.