In its ruling, a Catalan court said a payment of more than 5 million euros ($6.6 million) made by Jorge Horacio Messi, the Barcelona star's father, made it unlikely that either Messi or his father would withhold funds "during the legal process of a pending tax fraud trial."
The complaint, originally lodged by Raquel Amado, a state prosecutor for the northeastern region of Catalonia, alleged Messi tried to conceal the extent of his earnings and that he owed 4 million euros ($5.3 million) in back taxes.
"Given the global impact of professional footballer Lionel Andres Messi Cuccittini, and therefore his solvency," and the payment of 5,016,542.27 euros, an amount "the tax agency deems appropriate," the court threw out the bail request, the ruling said.
The court also said it was considering a request made by one of Messi's lawyers to postpone a court hearing set for Sept. 17. It said a ruling on a possible postponement would be announced soon.
The court statement said Messi's father made the payment, which was intended to cover alleged taxes outstanding plus interest, on Aug. 14.
Messi and his father are accused of allegedly defrauding the tax agency of income tax returns in 2007, 2008 and 2009.
Messi, who is rated by Forbes as the world's 10th highest-paid athlete, reportedly earned $41.3 million in the year to June; with $20.3 coming from his club salary and $21 million in endorsements. The 25-year-old Messi has won four straight world player of the year awards.
Spain has been cracking down on tax evasion as it fights to repair the country's public finances amid a prolonged recession and the collapse of its once-booming real estate sector.
Finance Minister Cristobal Montoro warned footballers in April they should make sure they are "comfortable" with their tax affairs.
Former Portugal star Luis Figo was last year forced to pay 2.45 million euros in income tax from his time at Barcelona. The tax authorities said the money was due from the 1997-99 period and pertained to his image rights.