Nadal had criticized Federer for his unwillingness to speak out on issues affecting the men's game, allowing others to "burn themselves" as they seek improved conditions for players.
After joining Nadal in the second round of the Australian Open with a win on Monday, Federer said "things are fine" between the two longtime rivals, although he concedes that they disagree on a way to resolve a list of player grievances that includes the length of the season and the distribution of prize money.
"We can't always agree on everything," Federer said. "So far it's always been no problem really. Back in the day he (Nadal) used to say, 'Whatever Roger decides, I'm fine with.'
"Today he's much more grown up. He has a strong opinion himself, which I think is great."
For his part, Nadal apologized for airing his disagreement with Federer in public -- although he didn't back down on the views he expressed.
"Probably I am wrong telling that to (the media), especially because these things can stay, must stay in the locker room," Nadal said.
"I always had fantastic relationship with Roger. I still have fantastic relationship with Roger. Just I said we can have different views about how the tour needs to work. That's all."
The rift emerged following a player meeting on Saturday that sparked talk of a possible strike for the second time in six months.
Nadal wasn't alone in questioning Federer's stance. Former No. 3-ranked Nikolay Davydenko said Monday he didn't understand why the 16-time Grand Slam champion wasn't supporting his fellow players.
The Russian said that while Nadal and No. 1-ranked Novak Djokovic had been leading the push for changes, Federer had been reluctant to get involved.
"I don't know why Roger is not supporting the players," Davydenko said. "Because he don't want ... any problems. He's nice guy. He's winning Grand Slams. He's from Switzerland. He's perfect.
"He don't want to do anything, he just try to be an outsider from this one."
However, Federer said his reluctance to speak out shouldn't be construed as a lack of support.
"I was in the meeting. I completely understand and support the players' opinions," Federer said. "I just have a different way of going at it. I'm not discussing it with you guys in the press room. It creates unfortunately sometimes negative stories."
The players plan to meet again at the Indian Wells Masters tournament in March when they will assess how much progress has been made before deciding on a course of action.
Davydenko said a strike remained a remote prospect, but that "the ATP should try to do something between now and Indian Wells." Federer wants to avoid such drastic action if possible.
"(Strike) is such a dangerous word to use," Federer said. "It's not good for anyone really. We've seen it in other sports happening in the States. That's why I'm always very careful about it.
"If there's no avoiding it, I'll support the rest of the players. But I just think we have to think it through how we do it, if we do it, can we do it, whatever it is, instead of just going out and screaming about it."
Federer said there are "two or three" big issues that the players have been discussing. They include the length of the season and prize money at Grand Slam tournaments, which some players believe has not increased proportionately with growing profits.
American John Isner said he had been to the meeting and felt the players had a "legitimate beef" over prize money, which is also an issue at the Indian Wells tournament, where Davydenko said those players who lose in the first round can sometimes lose money after paying tax and travel costs to compete.
Federer said he was confident "a good solution" would be reached and he welcomed the healthy debate. Nadal, meanwhile, vowed that he wouldn't be speaking about it in public again.
"I do not talk anymore," he said. "Yesterday (Sunday), I started, and I say I don't want to talk anymore about this. Finally I talked too much as usual. That's not going to happen again. You can try hard, but I'm going to talk about tennis."