The swimmers suffered from vomiting and abdominal cramps, while some even passed out on Sunday during competition at the Mon Repos pool, according to media reports.
A dozen, suffering from serious stomach flu, were transported to hospital for treatment, the 24heures newspaper said in an online report.
The pool has been closed until the results of tests are known, the daily said.
“The analyses are still under way,” Eric Renard, the president of the organizing committee for the Swiss swimming championships, told the newspaper.
“They could take days (to complete),” Renard said.
“The origin maybe viral, bacteriological or it could come from a toxin.”
Renard said he was sorry for all the affected swimmers.
A total of 460 swimmers from 54 different Swiss clubs were taking part in the competition.
A restaurant in the swimming complex was requisitioned to deal with those who had fallen ill.
Six ambulances, police officers and 20 fire fighters responded to calls for help.
“We are also waiting for the results of analyses to decide what measures to take,” Marc Vuilleumier, executive councillor in charge of sports for the city of Lausanne told 24heures.
“What we can say at this stage of the investigations is that there is no clear link that connects the people who were intoxicated.”