Catalan television station TV3 distributed footage of the Barca striker rubbing his face and talking to his father, also sitting on the accused bench, right before the begining of the session.
The trial began on Tuesday (May 31) although Messi missed the first and second days, which he was not obliged to attend, citing a back injury sustained in Argentina's international friendly with Honduras last Friday (May 27).
Lionel and Jorge Horacio Messi are accused by the Spanish tax office of defrauding the government of 4.2 million euros ($4.7 million) between 2007 and 2009.
They could face jail terms of up to 22 months if found guilty, although it is customary in Spain that offenders of non-violent crime with a sentence of under two years do not serve time in jail.
The case centres on the player's image rights and a web of shell companies allegedly used to evade taxes on income from those rights.
Tuesday's hearing showed that Spain's tax office made 20 inspections of Messi during its three-year investigation. According to the prosecutors' office, revenue was hidden using shell companies in Uruguay, Belize, Switzerland and the United Kingdom.
Messi and his father paid five million euros to the tax authorities as a "corrective" measure after being formally investigated in June 2013.
Spain's tax office has also begun investigating the finances of Messi's Barcelona team-mates Neymar Jr, Javier Mascherano and Adriano. Mascherano accepted a one-year prison sentence for tax evasion as part of a plea bargain in January, although is not expected to serve time in jail.
Messi moved to Barcelona from his birth place of Rosario, Argentina in 2000, becoming a Spanish citizen in 2005.
He is 10th on Forbes Magazine's list of the world's highest-earning athletes over the past decade, with an estimated income of $350 million.
Messi has scored 453 goals in 531 appearances for Barca in all competitions. He has also won eight La Liga titles, four King's Cups and four Champions League crowns with Barca, leading them to a league and cup double last season.
Messi is also captain of Argentina and will rejoin the team immediately after his court appearance to prepare for the Copa America in the USA, playing their first game against holders Chile on Jun. 7.
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