Nani suffered the injury before flying to South Africa
Portugal winger Nani, who was ruled out of the World Cup earlier in June after suffering an injury to his collar bone, says he will be "fine in a week".
Manchester United's Nani, 23, picked up the injury in training on 3 June in Lisbon before flying to South Africa, but was then declared unfit on 8 June.
A Portuguese Football Federation vice-president dismissed media suggestions there had been a disciplinary problem.
"There's no intention of hiding anything," said Amandio de Carvalho.
Nani, who scored three goals in 11 appearances during qualification, has been replaced in Portugal's squad by Benfica midfielder Ruben Amorim.
Amorim made 24 appearances for Benfica last season, helping the club to their first Portuguese title in five years.
Winger Nani had demonstrated impressive form for Manchester United during the second half of the 2009/10 season.
During the campaign he scored six goals in 34 appearances as United finished runners-up to Chelsea in the Premier League and reached the quarter-finals of the Champions League, where they were beaten on away goals by Bayern Munich.
He scored a superb chipped goal in Portugal's 3-1 victory over Cameroon in a home World Cup warm-up game on 1 June.
Portugal also have injury concerns over defender Pepe, who has been recovering from a knee injury he sustained in December.
The Real Madrid centre-back has not played since then but has been cleared by doctors from both his club and country to travel to the finals with a view to featuring at some stage.
Portugal's first match of the tournament is on 15 June against Ivory Coast in Group G, which also includes Brazil and North Korea.