Coach Carlos Queiroz said he still hopes Deco can recover for the team's final group match against Brazil.
Deco was Portugal's only player to skip training Sunday.
"At the training session yesterday, he complained about left hip pain," Queiroz said through a translator. "He's had this before.
"There was no improvement today, so our medical team recommended that he shouldn't play (Monday). But we do believe that he will play against Brazil."
Queiroz declined to say who would take the playmaker's place in the starting lineup. Portugal is already without Manchester United winger Nani, who was ruled out of the World Cup before the tournament started.
Deco was critical of Queiroz's tactics and substitutions after Portugal's 0-0 draw with Ivory Coast last week, calling them "strange" and "not as good as they might have been."
He later apologized.
A team official rejected suggestions that Deco's absence was related to his criticism of Queiroz's coaching.