Cyclists complained their performance had been affected as the competition in Singapore got under way with the men's and women's individual time trials.
"The Singapore Southeast Asian Games Organising Committee has received a report of an incident involving a bout of loose stools that has affected a few athletes early this morning," a statement said.
"We are investigating the matter with the relevant authorities and reinforcing hygiene practices."
The Straits Times newspaper said the cyclists were staying at Resorts World Sentosa, a hotel, casino and funpark complex popular with tourists.
"Two other riders, including my room-mate, are down too. I think it was the chicken and the curry egg at dinner. I felt sick at around 1am last night," he said.
The incident follows a food poisoning outbreak at the 2010 Youth Olympic Games in Singapore, which affected more than 20 people working for the organising committee.
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