Ruzicka, who was suspended immediately after the prosecutor's announcement, has been replaced on an interim basis by chief financial officer Andreas Boelte.
Comments from the prosecutor's office reported in the German press suggest there are accusations against a further eight people, including two Aegis staff.
However, no Aegis staff have been notified by the prosecutor that they are under investigation.
The focus of investigations is believed to be on embezzlement from Aegis itself, rather than from its clients.
A spokeswoman at Aegis' UK headquarters said: "The investigation relates to Aleksander Ruzicka personally. Aegis Media is not under investigation or suspicion and we are acting quickly and decisively to put in a new interim management team, communicate with clients and keep our staff in the picture."