World number two Nadal, along with Andy Murray, have been heavily critical of the ATP calender, claiming that it is too demanding on the top players in the world.
Federer has so far declined to pass comment on the situation, resulting in Nadal urging the Swiss player to use his influence in the game on the authorities.
"[Federer's position] is easy. Do not say anything, all positive, I am a 'gentleman', others get burned," Nadal told a press conference. "We each have our opinion and maybe he likes the circuit. Me too, I like it, and I think it's better than most sports. That does not mean you cannot be better and that you should change things that are bad.
"I say a lot of good things about tennis, because thanks to this sport I have had experiences in my life I could never have dreamed of, but to finish your career with pain in all areas of your body is not positive.
"He finishes his career as fresh as a daisy because he is physically privileged, but neither Murray nor (Novak) Djokovic and I are fresh as a daisy."
Nadal was speaking in Melbourne ahead of next week's Australian Open.