The USKOK police force said the actions had cost the state 12.2 million kuna ($1.84 million) in unpaid taxes and taken 116 million kuna from the club.
The three - as well as a tax official charged with helping tax evasion - were identified only by their initials in the online statement, in line with usual police practice.
But state television said they were former Dinamo chief executive Zdravko Mamic; his brother Zoran Mamic who is current Dinamo coach; and Damir Vrbanovic, a former Dinamo executive and the current top official of the Croatian football federation HNS.
All were briefly arrested last year during investigations into the same charges and all denied any wrong-doing at the time. None were immediately available for comment on Tuesday.
Zdravko Mamic resigned his position in Dinamo in February saying he wanted to secure a stable future for the club. He again insisted he was not guilty.
Dinamo won their 10th consecutive and 17th overall Croatian title last season. They top the table this season with 76 points after 33 out of 36 rounds, four points ahead of nearest rival Rijeka.
(Reporting by Igor Ilic; Editing by Andrew Heavens)
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