Ronaldo was called up by Portugal coach Carlos Queiroz for the two-legged FIFA World Cup play-off against Bosnia-Herzegovina despite Real insisting the player will not be fit to return to action for at least a fortnight.
The Spanish giants believed FIFA's regulations on the status and transfer of players for international duty gave Ronaldo the right to be assessed by the Portuguese federation's medical staff in Spain, but the player will now return home for a fitness check.
A statement on Real's official website read: "Real Madrid wishes to announce that Cristiano Ronaldo will travel to Portugal in the next few hours to put himself at the disposal of the medical services of the Portuguese federation."
Queiroz and the Portuguese federation (FPF) have now got their wish to perform their own assessment of the player, who suffered his injury playing for Real against Marseille in the UEFA Champions League on 30 September.
Last night Real Madrid sent medical documents to the Portuguese federation relating to Ronaldo's injury in a bid to end the dispute.
A statement issued by Madrid to Spanish sports newspaper Marca read: "On Monday we sent the Portuguese federation all the medical evidence, from both our physician and (Dutch specialist) Niek van Dijk, which indicated that Ronaldo is injured."
Queiroz defended his decision to ask Ronaldo to return to Portugal for assessment. "Based on the rules and principles governing clubs and associations, we have put Cristiano in the squad," he told Portuguese sports daily A Bola.
"Of course, I welcome that these principles have been met. I have always said that this is a technical decision and that everyone must be observed before being cleared to play. Cristiano and everyone will be observed. Our medical team are competent and responsible, and you will see what happens.
"I do not understand the nervousness in some sectors. It is a decision that is non-negotiable, unavoidable, a decision that protects the interests of the player.
"I was coach of Real. The club deserves respect; I know the medical team, president and CEO. I have every respect for that club. (But) this fact cannot compel me to put any club below or above the others. All clubs and players deserve equal treatment."