The Argentine wizard, who returned last month after a lengthy knee injury, is suffering from renal colic, a problem commonly caused by kidney stones.
"His future availability will depend on the outcome of further medical tests," said a statement on Barcelona's website.
Messi had appeared in good spirits since Barca arrived in Japan on Monday, joking with team-mates and signing autographs for local fans who turned out in their hundreds to watch their idols train.
Year in Review: When Messi and Barcelona conquered all
Brazilian striker Neymar, who has been in a rich vein of form this season, will also miss the game as he recovers from a groin strain suffered in Barca's European Champions League clash at Bayer Leverkusen earlier this month.
Luis Suarez, the third member of Barcelona's vaunted strike-force, starts.
European champions Barcelona are attempting to become the first side to win the Club World Cup three times.
The Catalan giants beat Argentina's 2-1 in 2009 and thrashed Brazil's Santos 4-0 two years later.
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