In an exclusive interview with Sky News, the Fifa president Sepp Blatter said the current post-Bosman practice of tying players to long contracts amounts to "modern slavery".
And he is urging Manchester United and Real Madrid "to sit together" if Ronaldo wants a move to the Spanish club.
"If the player wants to play somewhere else, then a solution should be found," said Blatter.
"Because if he stays in a club where he does not feel comfortable to play then it's no good for the player and for the club.
"I'm always in favour to protect the player and if the player wants to leave, let him leave."
Manchester United insists Ronaldo must stay to see out his contract and are expecting him to return to their Carrington training complex next week.
Since the landmark Bosman ruling, players are free to leave clubs when their deals are concluded.
But, says Blatter, that has inspired owners to tie footballers to long contracts so that the only way for them to leave is to pay up the remainder or get the buying club to do so.
He said: "I think in football there is too much modern slavery, transferring players or buying players here and there, and putting them somewhere. And we are trying now to intervene in such cases."
Asked if he felt sympathy for Ronaldo's current position, Blatter said: "Absolutely, absolutely".
He added: "Definitely as a footballer and the Fifa president, I'm very in sympathy with the player Ronaldo."
Blatter showed little sympathy in the face of the Premier League's recent efforts to stage an international round of games abroad.
And with England preparing its bid to stage the 2018 World Cup, Blatter has sent a warning to the FA to discourage further similar ideas.
The so-called 39th game controversy has not injured England's prospects of staging the tournament, he said.
But Blatter understands through his contacts that the Premier league may be preparing a second plan.
"My information is that what they want to do is perhaps to play some of the League Cup matches somewhere outside of England," he said.
When asked what he would advise the Premier League faced with such a plan, he said: "They should just forget about that."
The clear implication is that England are in pole position to stage the 2018 World Cup, against strong bidding contenders from the likes of Spain and Russia, but they need to keep the majority of the 24 Fifa delegates on side.
Blatter was keen to stress in the interview that only a natural catastrophe would deny South Africa its staging of the 2010 World Cup.
He revealed he has spoken to three countries that could stage the tournament with a year's notice. He would not rule out that one of those countries is England.
