In comments translated from French, Federer appeared to criticize Wawrinka's performances in the 5-0 first-round loss.
But speaking at a pre-tournament news conference Monday at the ABN Amro World Tennis Tournament in Rotterdam, Federer said there was no rift with Wawrinka.
"It was a tough weekend for us," he said. "I did have a day to sort of recover on Sunday and just weather the press because it was taken completely the wrong way, me blaming Stan. I would never do that and it was just an unfortunate weekend.
"There were many different circumstances leading to our defeat. First and foremost, I think the Americans played really well."
Playing at home on indoor clay, Federer and Wawrinka both lost their singles matches on the opening day against the U.S. before they also lost the doubles against Mardy Fish and Mike Bryan to seal the loss on Saturday.
"I'll move on quickly from here," Federer said, "because I had good conversations with the captain (Severin Luthi), with Stan himself obviously, and just making sure there's no misunderstandings."
After two losses in Davis Cup and a semifinal defeat to Rafael Nadal at the Australian Open last month, Federer is looking to bounce back in Rotterdam, where he is playing for the first time since winning the title in 2005.
He will play Nicolas Mahut of France in the first round.