Messi and his father, who have denied wrongdoing, have been accused of defrauding the Spanish state of more than 4 million euros (£3.21 million) by filing incomplete returns for the years 2007 to 2009.
Income from Messi's image rights was allegedly hidden using a web of shell companies in Uruguay, Belize, Switzerland and Britain.
"In actual fact I want to be quite cautious over this (topic)," Jorge Messi said in an interview with Spanish radio.
"I have always said it, he (Lionel) had absolutely nothing to do with it, so there is no need to talk about it.
"My lawyers are dealing with this issue so it's something with me and has nothing to do with him."
Lionel Messi has been resident in Barcelona since 2000 and gained Spanish citizenship in 2005.
He is one of the world's highest-paid athletes and earns just over $40 million (£25.07 million) a season in wages and bonuses, according to Forbes magazine.
He also pulls in some $23 million in endorsements from partners including Adidas, Samsung, PepsiCo and Turkish Airlines and is fourth on Forbes's latest list of top-earning athletes.
(Reporting by Iain Rogers, editing by Ian Ransom)
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