The 32-year-old midfielder was charged with "committing the criminal offence of giving false testimony" last June during a trial against Mamic and three others before a local tribunal, a prosecutors' statement said.
In line with Croatian law the prosecutors did not name Modric as the indictee but identified him as a "Croatian citizen born in 1985."
Local media identified him as Modric.
If found guilty, the Croatia captain faces up to five years in prison.
Cash was allegedly embezzled through fictitious deals related to player transfers. Modric testified last June over the details of his 2008 transfer from Dinamo to Tottenham Hotspur.
From there he joined Real Madrid in 2012.
The prosecutors charge Modric that, when questioned at the tribunal, he falsely said he had signed an annex to a contract with Dinamo over conditions for future transfers while still playing in Croatia.
Mamic is considered the most powerful man in Croatian football and his connections extend into many spheres of public life.
Most Croatian football fans see him as the real boss of the Croatian Football Federation and believe its formal chief Davor Suker is merely Mamic's puppet.
Modric, who grew up as a refugee in Zadar on the Dalmatian coast, was highly popular in Croatia where he has a reputation for modesty.
But the testimony has tarnished his image.
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