World No 3 Federer will be the second seed at the Grand Slam he has won eight times.
It means world No 2 Nadal will drop to third and will potentially have to beat both Federer and Novak Djokovic to clinch the title.
Grass court results from the previous two years are taken into consideration when Wimbledon name their seeds.
Nadal will definitely be in the same half as Djokovic or Federer, with the other then a likely final opponent.
But the Spaniard claims the All England Club “do not respect” the ranking he has earned over the last 12 months.
“They do not respect the status that some players have earned throughout the season,” Nadal told Movistar.
“It’s the same as always, Wimbledon is the only tournament of the year that does what they think in that sense, it’s their criteria.
“Whatever it is, whether I’m number two or number three I’ll have to play at my best.
“Obviously it is better to be number two than three but if they consider that I must be three, I will accept and fight to try to win the matches and compete well with the rivals.”
Nadal feels there should be consistency in seedings at the four major tournaments.
“The only thing that does not seem right about this story is that Wimbledon is the only one to do it, if they all did it it would seem right or correct,” he added.
“But when only one tournament does, not only in my particular case, it has happened many times other players in their own right.
“They have played well all year on different surfaces, have earned a status, that status is not respected.
“The only thing that affects me if I’m two or three is that if I’m three and I want to reach the final, Djokovic or Federer will be in my path.
“But that could only happen in the semi-finals and to get there I have to win five games.
“Today I’m far away, I do not think about it, I try to be in what I have to be, which is to arrive as well prepared as possible.”