A spokeswoman for the festival said Prenner had left for personal reasons and that the company was seeking an external applicant for the role. However, she said that no shortlist of candidates had yet been determined.
Roger Hatchuel, the Cannes chairman, has assumed the position of interim chief executive while a replacement is being sought.
Prenner, who is Austrian, took the job in January from Romain Hatchuel, who left to become the director of global new business at Euro RSCG.
Separately, the organisers have announced a ban on German judges in 2003, the 50th Cannes festival.
A statement sent to German advertising agencies warned of the ban. It alleged that 11 German advertising agencies had formed an "entente" which restricted how many awards they would enter as part of an attempt to cut costs.
Among the awards shows allegedly boycotted by the German cartel is Eurobest, also run by Roger Hatchuel.
The statement outlines three reasons condemning the "entente". It says it is illegal as it reduces competition. It continues: "It is unprofessional as the Eurobest Awards are handled in the same way as Cannes." The third reason is: "It is intolerable that, in a democracy, people cannot make their own choices of what to do or what not to do."
The Cannes spokeswoman said: "We have no comment on this - it is between us and Germany at the moment."