LaPresse club did not elaborate on the circumstances surrounding the decision, but the ANSA news agency said Manaudou does not get along with her trainer, Paolo Penso.
The club statement said Manaudou was informed about the decision while on vacation.
The team said she could return, but said the swimmer must first apologize to Penso and the French national team.
"There's one chance in a million for Laure to understand and come back," club president Marco Durante said in the statement.
Penso reportedly complained about Manaudou's performance at the meet.
"Today, we went back two or three steps on our path to the gold medal," Penso told French daily L'Equipe, referring to Manaudou's 12th-place finish in the 200 backstroke.
"I didn't like anything today ... after the first 50, she gave up."
Penso also expressed doubt about Manaudou's commitment to racing, and said that her lack of focus could affect future performances.
"I really think that the problem is in her head," Penso said. "I would like to know what she really wants to do. If she had problems to train hard for this race, this could be a problem for all the other races."
Manaudou split with French coach Philippe Lucas in May and moved to Turin, Italy. She is dating Italian swimmer Luca Marin.
Manaudou won the 400-meter freestyle at the 2004 Athens Olympics. At the World Championships in Melbourne, Australia, earlier this year she won the 200 and 400 free, plus three other medals.
Manaudou broke Janet Evans' 18-year-old 400 freestyle world record in May 2006.
"All of France's swimming world assures Laure Manaudou of its full support," French swimming federation president Francis Luyce told RTL radio, calling Manaudou "a key to success" for France at the Olympic Games in Beijing.
"I am confident that those who are responsible will find a solution to this mini-crisis," he said. He didn't rule out the possibility of Manaudou returning to Lucas if he would accept her back.