The head of the state Division of Public Health, Dr. Sandra Ford, said Monday that Candace Jones was placed on paid leave June 12. Jones has led the program for about two years.
Ford declined to identify the accusations.
Officials at the state Department of Community Health said the investigation focuses on mismanagement and failure to follow the law.
WIC is a $250 million federally funded program that provides monthly vouchers for supplemental foods such as cereal, eggs, juice, milk, peanut butter and infant formula. It serves about 300,000 people.