Ronaldo was left out of the national team announced on Thursday for upcoming worldwide matches, although his absence is not believed to be linked to the allegations that threaten the reputation of the five-time world player of the year.
Ronaldo was left off the squad for Portugal's second game in the Uefa Nations League at Poland on October 11 and a friendly match in Glasgow against Scotland three days later.
At a news conference on Thursday, Portugal coach Santos said Ronaldo had pledged continued commitment to the team, and that "in the future, nothing will prevent Ronaldo from contributing".
"Rape is an abominable crime that goes against everything that I am and believe in", the former Manchester United and Real Madrid star said.
He wrote: 'I firmly deny the accusations being issued against me.
The news comes amid the ongoing rape allegations against Portugal's record goalscorer, who was also left out of Fernando Santos' squad last month.
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'Keen as I may be to clear my name, I refuse to feed the media spectacle created by people seeking to promote themselves at my expense.
Santos said the decision was taken after a three-way conversation between him, Ronaldo and the head of the Portuguese FA.
"My clear conscious will thereby allow me to await with tranquillity the results of any and all investigations".
Despite the absence of the 33-year-old, Santos reaffirmed he will remain an integral part of the national team's plans going forward.
She signed a $375,000 settlement agreement, according to the suit, that required her silence on the matter though her lawyers said it should now be voided.
Ronaldo has made 154 appearances for Portugal and is their all-time top scorer.