The tournament will be played on blue clay for the first time, despite strong opposition from a number of top players, including Rafael Nadal.
Nadal recently quit his position as vice-president of the ATP player council in frustration at Federer's lack of support over proposed changes to the ranking system.
However, despite their conflicting views over the rankings system and the recent election of Brad Drewitt as ATP president, Federer is fully behind Nadal in opposing the new blue clay.
"I'm against it because Nadal is against it and we would have other options," Federer told Swiss journalist Rene Stauffer. "But tournament director Ion Tirias has insisted ad nauseam. In the end we said: He does a lot of good things for tennis so we let him go with this one. But it isn't good that he has such things in his hands."
"I have no idea how this will go. We were against it, Nadal even vehemently and I support him. He fears that a tradition is getting broken and that one tournament director wants to have blue clay, the other one grey, green or red one."
"I'm also for traditions but I can understand it that new things have to get tested. The clay in Madrid has to be perfect though otherwise it will be a debacle for the tournament."
While ATP player council president Federer supports Nadal in opposing the blue clay in Madrid, he insists it is not a reconciliatory effort in a bid to repair his relationship with the Spaniard, and he admitted the pair had not spent much time together.
"That has nothing to do with it," Federer said. "This topic has been talked about one year ago before our dissensions about the election of the new ATP president or the system of the world rankings."
He added: "We have seen each other not that often. He wasn't in Rotterdam and Dubai, I wasn't in Shanghai and he wasn't in Bercy. We only saw each other in London, Melbourne and briefly in Indian Wells. We have a bit more distance at the moment compared to times when we saw each other for weeks nearly daily."
"That's one of the reasons why there have occurred certain problems as we couldn't communicate that often. That shouldn't be an excuse though. But I also think it's normal that we have differences in opinion. I don't have a problem with Nadal no matter what he says or thinks."
Date: 28.04.2012, Source: ESPN