The US health and human services secretary, Michael Leavitt, said he had received a report of an outbreak of dysentery in Biloxi, Mississippi.
The lack of clean drinking water in parts of the Gulf coast region and standing floodwaters with decomposing bodies and human waste in the streets of New Orleans could cause a rash of infectious diseases, including West Nile virus and the often fatal E coli bacterium, he warned.
"All of the infectious diseases that occur when people are in large congregations of people can spread," Mr Leavitt said.
It was reported that officials had closed a shelter in Biloxi on Saturday because more than 20 people had fallen ill. Doctors believe the patients may have contracted dysentery from tainted water.
Another 20 people in the area were treated for vomiting and diarrhoea.
The shelter at a Biloxi school had been without water and power since Katrina hit on Monday. About 400 people had been staying there, and doctors said some may have ignored warnings to stay away from water.
Some running water came back late on Friday, but it was not safe to drink or even to use to brush teeth or wash, said Dr Jason Dees, a volunteer working at Biloxi regional medical centre.
Most of the patients were treated with antibiotics.
About 30 of the affected residents were taken to a hospital in Mobile, Alabama, while the rest were taken by bus to a shelter in Thomasville, Georgia.
Corporal Kayla Robert, of Biloxi police, said she had no idea what caused the illnesses.
"Who knows what they swallowed before they got here," she said.
"Half of them were swimming in stuff that we don't even know what it was."
Harrison county's health director, Bob Trabnicek, said: "It's not a disaster, it's a catastrophe."
Oliver Morgan, an epidemiologist at the London School of Hygiene and Tropical Medicine, told the Los Angeles Times that the threat of disease was not from the corpses but from those living in squalid conditions without clean water.
"After these big events where there are large numbers of fatalities, there is a rush to dispose of the dead and a lot of scare stories about imminent epidemics," he said.
"But the risk of disease transmission is really coming from the surviving population."
