No deaths have been reported but the outbreak spans 23 states and health authorities warned people not to eat fresh, whole papayas imported from Mexico by Agromed Produce of McAllen, Texas.
"Consumers should not eat recalled papayas, and restaurant and food service operators should not serve them," said the CDC.
The company issued a voluntary recall on Saturday of all Blondie, Yaya, Mananita, and Tastylicious Brand papayas sold prior to July 23 because they could be contaminated.
The first cases in the salmonella agona outbreak arose in January and have continued to be reported through mid-July, the CDC said. Twenty-five of the 99 illnesses have been in Texas, the worst hit US state.
In Mexico, the Agriculture Ministry said Tuesday that it was too soon to know if the Mexican papayas in question were the source of the illness.
US and Mexican authorities "are carrying out an investigation in both countries to determine the source of the outbreak of salmonella" so it is not time for any conclusive comment on cause, said Enrique Sanchez, who heads up Mexico's food safety agency.
"For now, Mexican papayas cannot be named as the source of the illness," Sanchez said.
Salmonella poisoning usually causes diarrhea, fever, and stomach pains within 12 to 72 hours of eating, and symptoms can last up to a week.
Most people recover without treatment, but people with weak immune systems, the elderly and the very young could be at risk if the infection spreads to the bloodstream.