The Mississippi boy, whose name was not reported, was visiting a home in Louisiana and may have come into contact with the deadly waterborne Naegleria fowleri amoeba while playing on a plastic toy water slide, Peralta said.
The Louisiana Department of Health and Hospitals said water samples taken from the home tested positive for the amoeba.
Out of caution, officials said the parish began on Thursday treating its water system with additional chlorine and flushing potentially contaminated water from its lines.
"We are working with the parish to make sure precautionary measures are being taken while we await additional test results on samples taken from the area's water system," Assistant Secretary for Public Health J.T. Lane said in a statement.
The boy's death is the second from the deadly amoeba in less than two weeks. Twelve-year-old Zachary Reyna, of Florida, died last month of the parasite.