The Spaniard has been a dominant force in the clay tournament over the last eight years, winning all but one since his first triumph in 2005.
However, having been out with an injury, Nadal has slipped down the rankings, leading to Roland Garros committee member Guy Forget to insist that the 26-year-old should be seeded higher.
The appeal has been rejected, but Federer believes that it won't make much difference.
"He's been so successful there in the last eight, nine years that everybody knows that he deserves it," said Federer.
"But it's not like he's ranked 80 in the world and he's going to bump into the seeds or bump into the top four or something like that.
"Is it really going to make a huge difference if he's five or one? Not a whole lot."
Federer last won the French Open in 2009.