Nadal confirmed yesterday he would not be taking part in the US Open after suffering from left knee tendinitis - the same injury which kept him out of this Cincinnati and Toronto Masters, and the Olympics, where he had been due to carry Spain's flag.
Federer - currently playing in the Cincinnati Masters as a prelude to the Open -said he'd been in contact with his on-court rival over the injury.
"It's not a surprise, because I wrote him and he told me it wasn't looking good at all," said the world's top-ranked player.
"I kind of saw it coming. But obviously when it's official it's disappointing for tennis, there's no doubt about it.
"I would love to have him in the draw. With 12 days before the Open you figure he might still have time to fix what he has to fix to get ready.
"If he pulls out that early before the Open, it must be something serious. That's what is sort of scary. There is obviously the whole debate going on if he is going come back for this year."
Nadal has not played since his shock second-round defeat by Lukas Rosol at Wimbledon in June, and has been dogged by knee problems throughout his career - though stresses the current problem is not related to his previous injuries.
""I am very sad to announce that I am still not ready to play and have to withdraw from this year's US Open in NYC," he said in a statement yesterday.
"I am sorry since I always found great crowds and great support, but I have to continue with my recuperation and preparation to be ready to play in the right conditions."
His absence from the tournament will mean Olympic gold medal winner Andy Murray overtaking Nadal as the world's number three in the rankings.
Murray, who had been dealing with a knee problem of his own over the last week or so, was sympathetic over Nadal's recovery.
"I'm disappointed for him, it's obviously tough," he said after his win over Sam Querrey in the second round of the Cincinnati Masters last night.
"He's had trouble with his knees in the past. So I hope he can rest, doesn't come back too early, and gets them fixed so he can get back to playing his best tennis."