The Manchester United legend was branded a "rat" by his former teammate in his bombshell interview with Piers Morgan but Rooney finds the comments "strange".
The former England captain said at Globe Soccer Awards in Dubai: "Well listen, Cristiano Ronaldo's a fantastic player and, as I've said before, he and Messi are the two best players probably to play the game.
"And again, it's not a criticism. What I've said is age comes to all of us, and Cristiano is obviously feeling now that he's finally had to deal with that."
Rooney, who now manages MLS club DC United, continued: "Obviously, he's done an interview, and it's gone global, and it's strange, some of the comments are strange.
"But I'm sure Manchester United will deal with it once they've seen the full interview, and they will take whatever action they need to take."
Ronaldo was angered that he was not allowed to leave United in the summer and Rooney recently suggested that the Portuguese international risked becoming an "unwanted distraction" for the Premier League club following his decision to walk off the pitch in the win over Tottenham last month.
He said: "I just think the things he has done from the start of the season; it is not acceptable for Manchester United. I've seen Roy Keane defending him. Roy wouldn't accept that. Roy wouldn't accept that at all. It is a distraction which Manchester United don't need at the minute, when they are trying to rebuild.
"For Cristiano, just get your head down and work and be ready to play when the manager needs you. If he does that, he will be an asset. If he doesn't, it will become an unwanted distraction."