"After five years of presidency Pape Diouf will leave his job. I want to congratulate him for his work at the club," Robert Louis-Dreyfus said in a statement without making clear whether he had been sacked or was quitting.
"He has been a great chairman who has done everything for Olympique Marseille. From a sporting point of view he lifted the club to the highest level in France."
Marseille finished second in Ligue 1 last season but have not gained any silverware since they won the European Cup in 1993.
"Unfortunately some differences of opinion have appeared and we cannot go on together," Louis-Dreyfus added.
"We have new challenges ahead of us. A new chairman will be named in the coming days."
Diouf had been in conflict with the club's supervisory board director Vincent Labrune, who is also Louis-Dreyfus's spokesman.
The chairman did not show up at a supervisory board meeting last week after being summoned, saying he was celebrating Marseille's under-16 title.
Diouf had gained support from the club's eight fan groups, who organised a petition to save his job.
His departure is likely to be followed by that of sports director Jose Anigo, who according to media reports had said he would not stay if Diouf left.
