Six players had money and possessions taken from their room in the aftermath of la Roja's 2-1 Confederations Cup win over Uruguay on June 16 and officials of the Golden Tulip Hotel consequently opened an investigation into the matter.
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"These are all lies. They are trying to complicate other people's lives. The football federation will take up this matter," Pique told Cadena Cope.
"This is all a very unpleasant and unwelcome experience. This situation will be resolved, though. Lies are always exposed at some point."
Spain are currently preparing for the semi-final match against Italy on Thursday, with the winner to face either Brazil or Uruguay in the tournament's finale.