Nadal criticised Federer on the eve of the Australian Open, claiming the 16-time grand slam title winner should be doing more to support growing complaints over the professional tour.
Nadal has long advocated changes to the playing schedule and last year said strike action could not be ruled out. On Sunday, the world number two said Federer, the ATP Player Council president, needs to support his colleagues.
And Davydenko, speaking after his five-set defeat to Flavio Cipolla in the first round on Monday, agreed that Federer was not taking a leading role over the issues at stake.
"I don't know why Roger doesn't support players. I don't know why. Because he doesn't do any problems. He's a nice guy," the Russian said.
"He's from Switzerland. He's perfect. He don't want to do anything. He just tried to be outside from this one," he added.
"But he was sitting in the (players') meeting (on Saturday). He just listened to everything and I think Sunday was meeting the top four guys. I don't know what happened there."
The Russian, who has slipped to 52 in the world rankings, said it was important for the players to have the backing from the likes of world number one Novak Djokovic and Nadal.
"For sure Federer doesn't want to do anything because he doesn't want to make any strike or something. Nadal, Djokovic is with the other players, the top 100 players," Davydenko said.
Players met new men's tour chief Brad Drewett in Melbourne on Saturday and are reportedly unhappy over Davis Cup scheduling and their share of prize money at the grand slam tournaments, among other issues.
In his unexpected outburst against long-time rival Federer, Nadal told Spanish media in Melbourne: "It's easy to say I do not say anything, everything is positive and I stay 'a gentleman' while others burn.
"We each have our opinion and perhaps he likes the circuit. I like it too and it is better than the majority of sports. But that does not mean it can't be better and that things which are bad cannot be changed."