Portugal captain Ronaldo has a knock to the left thigh, while Pepe is struggling with a sprained left ankle, according to a statement released by the Portuguese Football Federation (FPF) on Monday.
"The two players are following specific treatment programmes for the next two days (Monday and Tuesday) and are due to return to training on Wednesday," added the FPF statement.
The duo teamed up with Paulo Bento's squad at their base in the town of Obidos in central Portugal ahead of their opening 2014 World Cup qualifying Group F fixtures in Luxembourg on Friday and at home to Azerbaijan in Braga next Tuesday.
Ronaldo was substituted in the second half of Madrid's 3-0 win against Granada in La Liga on Sunday evening.
He later created a media storm in Spain after telling reporters that he was "a bit sad" at the Santiago Bernabeu for "professional reasons."
However, he refused to speak to journalists gathered at Portugal's training base.
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