The 35-year-old captain, who is playing in his sixth and final World Cup, was reportedly kept apart as a "precautionary" step because of muscle exhaustion, according to Argentine media.
On Friday, Messi and a few other players remained in the gym rather than attending main training at the Qatar University, where his squad is one of the favourites in Qatar to win the one big prize that has escaped him throughout his stellar career.
Messi missed a Paris St Germain game earlier this month due to an inflamed Achilles tendon. But Argentinian media said there was no real doubt that he would miss the Saudi Arabia game.
Argentina will also face Mexico and Poland in Group C.
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