Ronaldo left the Portugal camp following a dispute with new coach Jorge Jesus over his lack of playing time in the Nations League after he was promised 30 minutes against Norway, but was instead kept on the bench.
He later apologised to his teammates and said in a statement that he would accept any punishment as the Portuguese federation reportedly prepare a fine and suspension.
Under federation rules, players who fail to appear for international duty face a severe ban ranging from one to six months, alongside a significant financial penalty.
Rooney, reigniting the drama, spoke up on his former teammate and his behaviour, which he has deemed uncomfortable and wrong.
"My thoughts on Ronaldo is just: 'Why?' It was the same day (Lionel) Messi was retiring from Argentina and for him to come out of the Portugal squad in that way, then put that statement out... It's just wrong in every sense.
"To undermine your manager, undermine your teammates the way he has - it was just so wrong. To undermine the Portuguese FA, everything about it was just wrong. From a football point of view, from being a teammate and a manager, it wasn't nice to see.
"It comes to every player. You have to finish international football and unfortunately he's not dealing with it well. It's uncomfortable to see.
"You can't tell a manager what he's got to say. That just goes beyond anything I've ever seen."
Ronaldo, now 41 years old, has not announced his retirement from international football as he chases down 1000 goals. Currently he is on 981, 19 short of 1000 and he will not stop until he reaches his goal in the twilight of his career.