Messi endured a quiet night in the 0-0 draw with the Netherlands on Wednesday, failing to register a single touch inside the opposition penalty area during the 120 minutes of play.
Likewise, Flick, who is coach Joachim Low's assistant, says that Die Mannschaft have also hatched a ploy to combat the Barcelona ace but refuses to divulge the strategy.
"We saw how the Dutch managed to keep Messi out, but we too have a special plan for him, although I won't give that away," he told reporters.
"We're looking forward to meeting a compact, organised team and in Messi, they have one of the outstanding players of the tournament."
Sunday's encounter at the Maracana kicks off at 8pm.