Mihalj Kertes, former customs chief and one of the late president's key aides, was indicted for abuse of position and embezzlement by Serbia's special court for organized crime.
The indictment against Kertes alleges that he acted on Milosevic's orders and illegally transferred millions of dollars of state money to Cyprus and dozens of offshore accounts elsewhere during U.N. sanctions in the 1990s.
Milosevic was also initially indicted but he died last year while in custody of the U.N. war crimes tribunal for former Yugoslavia.
Another Milosevic aide, former vice-premier Nikola Sainovic, was also charged in Serbia, but the trial against him was postponed because of proceedings before the Netherlands-based U.N. court. Sainovic is on trial there over his alleged role in atrocities in Kosovo during the 1998-99 war.